Functional ANnoTation Of the Mammalian genome Database
Names
More detailed information about this field from each metasource.
Functional ANnoTation Of the Mammalian genome Database
metasource: Fairsharing.org
version: None
FANTOM5
metasource: Fairsharing.org
version: None
metasource: re3data.org
version: re3data.org: FANTOM; editing status 2021-10-04; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3JG8M last accessed: 2022-11-04
FANTOM
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: FANTOM; editing status 2021-10-04; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3JG8M last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:05.943295
FANTOM DB
metasource: re3data.org
version: re3data.org: FANTOM; editing status 2021-10-04; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3JG8M last accessed: 2022-11-04
Functional ANnotation Of the Mammalian genome
metasource: re3data.org
version: re3data.org: FANTOM; editing status 2021-10-04; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3JG8M last accessed: 2022-11-04
SSTAR
metasource: re3data.org
version: re3data.org: FANTOM; editing status 2021-10-04; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3JG8M last accessed: 2022-11-04
fantom
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:05.943295
Names
More detailed information about this field from each metasource.
Functional ANnoTation Of the Mammalian genome Database
metasource: Fairsharing.orgversion: None
FANTOM5
metasource: Fairsharing.orgversion: None
metasource: re3data.org
version: re3data.org: FANTOM; editing status 2021-10-04; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3JG8M last accessed: 2022-11-04
FANTOM
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: FANTOM; editing status 2021-10-04; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3JG8M last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:05.943295
FANTOM DB
metasource: re3data.orgversion: re3data.org: FANTOM; editing status 2021-10-04; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3JG8M last accessed: 2022-11-04
Functional ANnotation Of the Mammalian genome
metasource: re3data.orgversion: re3data.org: FANTOM; editing status 2021-10-04; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3JG8M last accessed: 2022-11-04
SSTAR
metasource: re3data.orgversion: re3data.org: FANTOM; editing status 2021-10-04; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3JG8M last accessed: 2022-11-04
fantom
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:05.943295
Other names: FANTOM5, FANTOM, FANTOM DB, Functional ANnotation Of the Mammalian genome, SSTAR, fantom
Names
More detailed information about this field from each metasource.
Functional ANnoTation Of the Mammalian genome Database
metasource: Fairsharing.orgversion: None
FANTOM5
metasource: Fairsharing.orgversion: None
metasource: re3data.org
version: re3data.org: FANTOM; editing status 2021-10-04; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3JG8M last accessed: 2022-11-04
FANTOM
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: FANTOM; editing status 2021-10-04; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3JG8M last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:05.943295
FANTOM DB
metasource: re3data.orgversion: re3data.org: FANTOM; editing status 2021-10-04; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3JG8M last accessed: 2022-11-04
Functional ANnotation Of the Mammalian genome
metasource: re3data.orgversion: re3data.org: FANTOM; editing status 2021-10-04; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3JG8M last accessed: 2022-11-04
SSTAR
metasource: re3data.orgversion: re3data.org: FANTOM; editing status 2021-10-04; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3JG8M last accessed: 2022-11-04
fantom
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:05.943295
FANTOM (Functional ANnoTation Of the Mammalian genome) is a worldwide collaborative project aiming at identifying all functional elements in mammalian genomes.
Description
More detailed information about this field from each metasource.
FANTOM (Functional ANnoTation Of the Mammalian genome) is a worldwide collaborative project aiming at identifying all functional elements in mammalian genomes.
metasource: Fairsharing.orgversion: None
Functional annotation of mouse full-length cDNA clones
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
FANTOM stands for 'Functional Annotation of the Mammalian Genome' and is the name of an international research consortium organized by the RIKEN Omics Science Center. The FANTOM5 project aims to build a full understanding of transcriptional regulation in a human system by generating transcriptional regulatory networks that define every human cell type.
metasource: re3data.orgversion: re3data.org: FANTOM; editing status 2021-10-04; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3JG8M last accessed: 2022-11-04
The Functional Annotation Of the Mammalian Genome is a database for the transcriptional network that regulates macrophage differentiation. Data comes from cap analysis of gene expression, sequencing mRNA 5-ends with a second-generation sequencer to quantify promoter activities even in the absence of gene annotation. Additional genome-wide experiments complement the setup including short RNA sequencing, microarray gene expression profiling on large-scale perturbation experiments.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:05.943295
Webpage:
http://fantom.gsc.riken.jpWebpage
More detailed information about this field from each metasource.
http://fantom.gsc.riken.jp
metasource: Fairsharing.orgversion: None
http://fantom.gsc.riken.jp/
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
https://fantom.gsc.riken.jp/
metasource: re3data.orgversion: re3data.org: FANTOM; editing status 2021-10-04; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3JG8M last accessed: 2022-11-04
http://fantom.gsc.riken.jp/4/
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:05.943295
Licence:
Name: Creative Commons Attribution 4.0 International (CC BY 4.0)Licence name
More detailed information about this field from each metasource.
Creative Commons Attribution 4.0 International (CC BY 4.0)
metasource: Fairsharing.orgversion: None
Copyrights
metasource: re3data.orgversion: re3data.org: FANTOM; editing status 2021-10-04; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3JG8M last accessed: 2022-11-04
Licence URL
More detailed information about this field from each metasource.
https://creativecommons.org/licenses/by/4.0/
metasource: Fairsharing.orgversion: None
https://www.riken.jp/en/terms/
metasource: re3data.orgversion: re3data.org: FANTOM; editing status 2021-10-04; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3JG8M last accessed: 2022-11-04
Publications:
Publications
More detailed information about this field from each metasource.
Gateways to the FANTOM5 promoter level mammalian expression atlas
PMID: 25723102
metasource: Fairsharing.org
version: None
Update of the FANTOM web resource: expansion to provide additional transcriptome atlases
PMID: 30407557
metasource: Fairsharing.org
version: None
Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation
PMID: 21075797
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:05.943295
FANTOM DB: database of Functional Annotation of RIKEN Mouse cDNA Clones
PMID: 11752270
metasource: Fairsharing.org
version: None
https://doi.org/10.1093/nar/gkaa1054
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Publications
More detailed information about this field from each metasource.
Gateways to the FANTOM5 promoter level mammalian expression atlas
PMID: 25723102
metasource: Fairsharing.org
version: None
Update of the FANTOM web resource: expansion to provide additional transcriptome atlases
PMID: 30407557
metasource: Fairsharing.org
version: None
Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation
PMID: 21075797
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:05.943295
FANTOM DB: database of Functional Annotation of RIKEN Mouse cDNA Clones
PMID: 11752270
metasource: Fairsharing.org
version: None
https://doi.org/10.1093/nar/gkaa1054
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
-
Gateways to the FANTOM5 promoter level mammalian expression atlas
PubMed citations: 317.
317 articles citing: Gateways to the FANTOM5 promoter level mammalian expression atlas
3DFAACTS-SNP: using regulatory T cell-specific epigenomics data to uncover candidate mechanisms of type 1 diabetes (T1D) risk. PMID:35773720
The genes controlling normal function of citrate and spermine secretion are lost in aggressive prostate cancer and prostate model systems. PMID:35707723
Heterogeneity of enhancers embodies shared and representative functional groups underlying developmental and cell type-specific gene regulation. PMID:35680026
Somatic point mutations are enriched in non-coding RNAs with possible regulatory function in breast cancer. PMID:35672401
The Ramp Atlas: facilitating tissue and cell-specific ramp sequence analyses through an intuitive web interface. PMID:35664804
Neuronal Cells Display Distinct Stability Controls of Alternative Polyadenylation mRNA Isoforms, Long Non-Coding RNAs, and Mitochondrial RNAs. PMID:35664307
Whole exome sequencing identifies novel germline variants of SLC15A4 gene as potentially cancer predisposing in familial colorectal cancer. PMID:35562597
Asymmetric Predictive Relationships Across Histone Modifications. PMID:35529103
A systems genomics approach to uncover patient-specific pathogenic pathways and proteins in ulcerative colitis. PMID:35484353
microRNA-27b regulates hepatic lipase enzyme LIPC and reduces triglyceride degradation during hepatitis C virus infection. PMID:35483451
Comprehensive enhancer-target gene assignments improve gene set level interpretation of genome-wide regulatory data. PMID:35473573
DNA methylation profile of liver tissue in end-stage cholestatic liver disease. PMID:35473391
Blood Transcriptome Analysis of Septic Patients Reveals a Long Non-Coding Alu-RNA in the Complement C5a Receptor 1 Gene. PMID:35447887
Sincast: a computational framework to predict cell identities in single-cell transcriptomes using bulk atlases as references. PMID:35362513
Transcriptional atlas analysis from multiple tissues reveals the expression specificity patterns in beef cattle. PMID:35351103
Improving reusability along the data life cycle: a regulatory circuits case study. PMID:35346379
Comprehensive bioinformatic analysis reveals oncogenic role of H2A.Z isoforms in cervical cancer progression. PMID:35317119
Sequencing of individual barcoded cDNAs using Pacific Biosciences and Oxford Nanopore Technologies reveals platform-specific error patterns. PMID:35301264
Simple method for cutoff point identification in descriptive high-throughput biological studies. PMID:35287573
Immunostimulatory Cancer-Associated Fibroblast Subpopulations Can Predict Immunotherapy Response in Head and Neck Cancer. PMID:35262677
Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue. PMID:35256815
Dynamic control of chromatin-associated m6A methylation regulates nascent RNA synthesis. PMID:35219383
Prioritization of putatively detrimental variants in euploid miscarriages. PMID:35132093
Mouse genomic and cellular annotations. PMID:35124726
Combined inhibition of XIAP and BCL2 drives maximal therapeutic efficacy in genetically diverse aggressive acute myeloid leukemia. PMID:35121960
Characterization of the COPD alveolar niche using single-cell RNA sequencing. PMID:35078977
Distribution of alternative untranslated regions within the mRNA of the CELF1 splicing factor affects its expression. PMID:34996980
Regulatory Variant rs2535629 in ITIH3 Intron Confers Schizophrenia Risk By Regulating CTCF Binding and SFMBT1 Expression. PMID:34978167
Genomic environments scale the activities of diverse core promoters. PMID:34961747
Large-Scale Tissue Microarray Evaluation Corroborates High Specificity of High-Level Arginase-1 Immunostaining for Hepatocellular Carcinoma. PMID:34943588
Multiplexed activation in mammalian cells using a split-intein CRISPR/Cas12a based synthetic transcription factor. PMID:34908140
CoRE-ATAC: A deep learning model for the functional classification of regulatory elements from single cell and bulk ATAC-seq data. PMID:34898596
Carboxypeptidase A1 (CPA1) Immunohistochemistry Is Highly Sensitive and Specific for Acinar Cell Carcinoma (ACC) of the Pancreas. PMID:34889867
Natural SINEUP RNAs in Autism Spectrum Disorders: RAB11B-AS1 Dysregulation in a Neuronal CHD8 Suppression Model Leads to RAB11B Protein Increase. PMID:34880900
Mitochondrial Uncoupling Proteins (UCPs) as Key Modulators of ROS Homeostasis: A Crosstalk between Diabesity and Male Infertility? PMID:34829617
Integrative Omics Analysis Unravels Microvascular Inflammation-Related Pathways in Kidney Allograft Biopsies. PMID:34795664
Genome-wide CRISPR interference screen identifies long non-coding RNA loci required for differentiation and pluripotency. PMID:34731163
OncoDB: an interactive online database for analysis of gene expression and viral infection in cancer. PMID:34718715
Systems Analysis Reveals Ageing-Related Perturbations in Retinoids and Sex Hormones in Alzheimer's and Parkinson's Diseases. PMID:34680427
Tree-Based Co-Clustering Identifies Chromatin Accessibility Patterns Associated With Hematopoietic Lineage Structure. PMID:34659332
scMRMA: single cell multiresolution marker-based annotation. PMID:34648021
Dichotomy in the Impact of Elevated Maternal Glucose Levels on Neonatal Epigenome. PMID:34633450
Association Between Posttraumatic Stress Disorder and Epigenetic Age Acceleration in a Sample of Twins. PMID:34629427
Eosinophil extracellular traps drive asthma progression through neuro-immune signals. PMID:34616019
Krueppel-Like Factor 4 Expression in Phagocytes Regulates Early Inflammatory Response and Disease Severity in Pneumococcal Pneumonia. PMID:34589087
Unraveling the functional role of DNA demethylation at specific promoters by targeted steric blockage of DNA methyltransferase with CRISPR/dCas9. PMID:34588447
Transcription factors Krüppel-like factor 4 and paired box 5 regulate the expression of the Grainyhead-like genes. PMID:34570823
Leveraging the Cell Ontology to classify unseen cell types. PMID:34548483
DDX3X and DDX3Y are redundant in protein synthesis. PMID:34535544
A comprehensive integrated post-GWAS analysis of Type 1 diabetes reveals enhancer-based immune dysregulation. PMID:34529725
Candidate host epigenetic marks predictive for HIV reservoir size, responsiveness to latency reversal, and viral rebound. PMID:34482353
TANC1 methylation as a novel biomarker for the diagnosis of patients with anti-tuberculosis drug-induced liver injury. PMID:34465797
Introducing Thioredoxin-Related Transmembrane Proteins: Emerging Roles of Human TMX and Clinical Implications. PMID:34465218
Seeing the forest through the trees: prioritising potentially functional interactions from Hi-C. PMID:34454581
Transcriptional Regulation of RUNX1: An Informatics Analysis. PMID:34440349
TERA-Seq: true end-to-end sequencing of native RNA molecules for transcriptome characterization. PMID:34428294
ZSWIM7 Is Associated With Human Female Meiosis and Familial Primary Ovarian Insufficiency. PMID:34402903
Transposable elements and their KZFP controllers are drivers of transcriptional innovation in the developing human brain. PMID:34400477
Susceptibility loci and polygenic architecture highlight population specific and common genetic features in inguinal hernias: genetics in inguinal hernias. PMID:34392144
Pattern of placental alkaline phosphatase (PLAP) expression in human tumors: a tissue microarray study on 12,381 tumors. PMID:34363325
Dynamic chromatin regulatory landscape of human CAR T cell exhaustion. PMID:34285077
Telomere-to-telomere assembly of a fish Y chromosome reveals the origin of a young sex chromosome pair. PMID:34253240
Description of a CSF-Enriched miRNA Panel for the Study of Neurological Diseases. PMID:34206241
Epigenetic and Transcriptional Control of the Opioid Prodynorphine Gene: In-Depth Analysis in the Human Brain. PMID:34200173
Selection and thermostability suggest G-quadruplexes are novel functional elements of the human genome. PMID:34187812
Topological Analysis of Regulatory Networks Reveals Functionally Key Genes and miRNAs Involved in the Differentiation of Mesenchymal Stem Cells. PMID:34179189
Spearheading future omics analyses using dyngen, a multi-modal simulator of single cells. PMID:34168133
Potential Novel Genes for Late-Onset Alzheimer's Disease in East-Asian Descent Identified by APOE-Stratified Genome-Wide Association Study. PMID:34151794
An AIB1 Isoform Alters Enhancer Access and Enables Progression of Early-Stage Triple-Negative Breast Cancer. PMID:34135000
Fine-mapping, trans-ancestral and genomic analyses identify causal variants, cells, genes and drug targets for type 1 diabetes. PMID:34127860
Similarities and Differences in Gene Expression Networks Between the Breast Cancer Cell Line Michigan Cancer Foundation-7 and Invasive Human Breast Cancer Tissues. PMID:34056582
Common DNA methylation dynamics in endometriod adenocarcinoma and glioblastoma suggest universal epigenomic alterations in tumorigenesis. PMID:34021236
MIR-NATs repress MAPT translation and aid proteostasis in neurodegeneration. PMID:34012113
Genome-wide analysis of primary microRNA expression using H3K36me3 ChIP-seq data. PMID:33995896
Expression of Human Endogenous Retroviruses in Systemic Lupus Erythematosus: Multiomic Integration With Gene Expression. PMID:33986751
Landscape of allele-specific transcription factor binding in the human genome. PMID:33980847
Uncovering genetic mechanisms of hypertension through multi-omic analysis of the kidney. PMID:33958779
The phenotypic spectrum associated with OTX2 mutations in humans. PMID:33950863
Learning a genome-wide score of human-mouse conservation at the functional genomics level. PMID:33941776
GAPGOM-an R package for gene annotation prediction using GO Metrics. PMID:33931103
Mesothelin Expression in Human Tumors: A Tissue Microarray Study on 12,679 Tumors. PMID:33917081
A 127 kb truncating deletion of PGRMC1 is a novel cause of X-linked isolated paediatric cataract. PMID:33867527
DNA methylation signatures in cord blood associated with birthweight are enriched for dmCpGs previously associated with maternal hypertension or pre-eclampsia, smoking and folic acid intake. PMID:33784941
A two-stream convolutional neural network for microRNA transcription start site feature integration and identification. PMID:33707582
Prioritizing non-coding regions based on human genomic constraint and sequence context with deep learning. PMID:33686085
LAMA: automated image analysis for the developmental phenotyping of mouse embryos. PMID:33574040
A 44-kb deleted-type copy number variation is associated with decreasing complement component activity and calf mortality in Japanese Black cattle. PMID:33549039
H3K27me3-rich genomic regions can function as silencers to repress gene expression via chromatin interactions. PMID:33514712
A spatially resolved brain region- and cell type-specific isoform atlas of the postnatal mouse brain. PMID:33469025
Integrating comprehensive functional annotations to boost power and accuracy in gene-based association analysis. PMID:33320851
A flexible computational pipeline for research analyses of unsolved clinical exome cases. PMID:33303739
Complex genetic dependencies among growth and neurological phenotypes in healthy children: Towards deciphering developmental mechanisms. PMID:33270668
Linkage analysis identifies an isolated strabismus locus at 14q12 overlapping with FOXG1 syndrome region. PMID:33257509
DIANA-miRGen v4: indexing promoters and regulators for more than 1500 microRNAs. PMID:33245765
Accessing NCBI data using the NCBI Sequence Viewer and Genome Data Viewer (GDV). PMID:33239395
Dimeric Structure of the Pseudokinase IRAK3 Suggests an Allosteric Mechanism for Negative Regulation. PMID:33238146
ZNF354C is a transcriptional repressor that inhibits endothelial angiogenic sprouting. PMID:33154469
The PVT1 lncRNA is a novel epigenetic enhancer of MYC, and a promising risk-stratification biomarker in colorectal cancer. PMID:33148262
Analysis of splice variants of the human protein disulfide isomerase (P4HB) gene. PMID:33148170
The Fuchs corneal dystrophy-associated CTG repeat expansion in the TCF4 gene affects transcription from its alternative promoters. PMID:33116252
Single-Cell Profiling of AKI in a Murine Model Reveals Novel Transcriptional Signatures, Profibrotic Phenotype, and Epithelial-to-Stromal Crosstalk. PMID:33115917
Bioinformatic characterization of angiotensin-converting enzyme 2, the entry receptor for SARS-CoV-2. PMID:33112891
Expression of Calcification and Extracellular Matrix Genes in the Cardiovascular System of the Healthy Domestic Sheep (Ovis aries). PMID:33101359
Distinctive regulatory architectures of germline-active and somatic genes in C. elegans. PMID:33093068
Molecular Insights Into Regulatory T-Cell Adaptation to Self, Environment, and Host Tissues: Plasticity or Loss of Function in Autoimmune Disease. PMID:33072063
Nonmuscle myosin-2 contractility-dependent actin turnover limits the length of epithelial microvilli. PMID:33026933
Genome-Wide Association Analysis of Neonatal White Matter Microstructure. PMID:33009551
Stable gene expression for normalisation and single-sample scoring. PMID:32997146
Integrated regulatory models for inference of subtype-specific susceptibilities in glioblastoma. PMID:32974985
Comprehensive genomic analysis reveals dynamic evolution of endogenous retroviruses that code for retroviral-like protein domains. PMID:32963593
Sources of variation in cell-type RNA-Seq profiles. PMID:32956417
Evaluating the informativeness of deep learning annotations for human complex diseases. PMID:32943643
Expression profiling of WD40 family genes including DDB1- and CUL4- associated factor (DCAF) genes in mice and human suggests important regulatory roles in testicular development and spermatogenesis. PMID:32867693
Cis and trans effects differentially contribute to the evolution of promoters and enhancers. PMID:32819422
SOX10-regulated promoter use defines isoform-specific gene expression in Schwann cells. PMID:32770939
Predictive features of gene expression variation reveal mechanistic link with differential expression. PMID:32767663
The intersectional genetics landscape for humans. PMID:32761099
Quantitative characterization of tumor cell-free DNA shortening. PMID:32650715
Early evidence of delayed oligodendrocyte maturation in the mouse model of mucolipidosis type IV. PMID:32586947
CYP2J2 Molecular Recognition: A New Axis for Therapeutic Design. PMID:32534953
BICORN: An R package for integrative inference of de novo cis-regulatory modules. PMID:32409786
Complex Analysis of Retroposed Genes' Contribution to Human Genome, Proteome and Transcriptome. PMID:32408516
The DNA methylation landscape of human cancer organoids available at the American type culture collection. PMID:32396494
Treatable traits and therapeutic targets: Goals for systems biology in infectious disease. PMID:32363252
Human papillomavirus E7 binds Oct4 and regulates its activity in HPV-associated cervical cancers. PMID:32298395
Accelerated evolution of an Lhx2 enhancer shapes mammalian social hierarchies. PMID:32238901
CDK1 dependent phosphorylation of hTERT contributes to cancer progression. PMID:32214089
Resolving the 3D Landscape of Transcription-Linked Mammalian Chromatin Folding. PMID:32213323
Fibroblast growth factor receptor 1 gene amplification and protein expression in human lung cancer. PMID:32207251
Epigenetic modulation of AREL1 and increased HLA expression in brains of multiple system atrophy patients. PMID:32151281
A putative silencer variant in a spontaneous canine model of retinitis pigmentosa. PMID:32150541
Identification of methylation states of DNA regions for Illumina methylation BeadChip. PMID:32138668
Long non-coding RNAs in development and disease: conservation to mechanisms. PMID:32100288
Global analysis of LARP1 translation targets reveals tunable and dynamic features of 5' TOP motifs. PMID:32094190
Genome-wide characterization of 5-hydoxymethylcytosine in melanoma reveals major differences with nevus. PMID:32017278
HMGA2 Antisense Long Non-coding RNAs as New Players in the Regulation of HMGA2 Expression and Pancreatic Cancer Promotion. PMID:32010621
Transcriptomic and open chromatin atlas of high-resolution anatomical regions in the rhesus macaque brain. PMID:31980617
Virus-induced transposable element expression up-regulation in human and mouse host cells. PMID:31964680
Identification and transfer of spatial transcriptomics signatures for cancer diagnosis. PMID:31931856
Directional association test reveals high-quality putative cancer driver biomarkers including noncoding RNAs. PMID:31888644
Investigating the role of super-enhancer RNAs underlying embryonic stem cell differentiation. PMID:31888456
Topological structure analysis of chromatin interaction networks. PMID:31881819
Generation of Retinaldehyde for Retinoic Acid Biosynthesis. PMID:31861321
Enhancers Facilitate the Birth of De Novo Genes and Gene Integration into Regulatory Networks. PMID:31845961
Maintenance of active chromatin states by HMGN2 is required for stem cell identity in a pluripotent stem cell model. PMID:31831052
PsyMuKB: An Integrative De Novo Variant Knowledge Base for Developmental Disorders. PMID:31809863
Hepatocyte gene expression and DNA methylation as ancestry-dependent mechanisms in African Americans. PMID:31798965
Transcriptional control by enhancers and enhancer RNAs. PMID:31791217
Personalised analytics for rare disease diagnostics. PMID:31754101
A network-based approach to identify deregulated pathways and drug effects in metabolic syndrome. PMID:31740673
Pan-cancer RNA-seq data stratifies tumours by some hallmarks of cancer. PMID:31730267
Characterization of novel primary miRNA transcription units in human cells using Bru-seq nascent RNA sequencing. PMID:31709421
Whole Genome Sequencing of Familial Non-Medullary Thyroid Cancer Identifies Germline Alterations in MAPK/ERK and PI3K/AKT Signaling Pathways. PMID:31614935
Experimental and Computational Approaches to Direct Cell Reprogramming: Recent Advancement and Future Challenges. PMID:31581647
The WWOX Gene Influences Cellular Pathways in the Neuronal Differentiation of Human Neural Progenitor Cells. PMID:31543760
Deconvolution of transcriptional networks identifies TCF4 as a master regulator in schizophrenia. PMID:31535015
Quantifying the RNA cap epitranscriptome reveals novel caps in cellular and viral RNA. PMID:31504804
Quantifying the contribution of sequence variants with regulatory and evolutionary significance to 34 bovine complex traits. PMID:31501319
Whole-Genome Sequencing of Childhood Cancer Survivors Treated with Cranial Radiation Therapy Identifies 5p15.33 Locus for Stroke: A Report from the St. Jude Lifetime Cohort Study. PMID:31462438
Complex Phenotypes: Mechanisms Underlying Variation in Human Stature. PMID:31441021
Repression of ferritin light chain translation by human eIF3. PMID:31414986
Data-driven characterization of molecular phenotypes across heterogeneous sample collections. PMID:31329928
Discovery of a novel long noncoding RNA overlapping the LCK gene that regulates prostate cancer cell growth. PMID:31253147
Identification of Differential Roles of MicroRNA-33a and -33b During Atherosclerosis Progression With Genetically Modified Mice. PMID:31242815
The immune cell landscape in kidneys of patients with lupus nephritis. PMID:31209404
ATP6V0d2 controls Leishmania parasitophorous vacuole biogenesis via cholesterol homeostasis. PMID:31199856
Dynamic UTR Usage Regulates Alternative Translation to Modulate Gap Junction Formation during Stress and Aging. PMID:31141695
Impact of Colon-Specific DNA Methylation-Regulated Gene Modules on Colorectal Cancer Patient Survival. PMID:31083646
Large-scale in-silico identification of a tumor-specific antigen pool for targeted immunotherapy in triple-negative breast cancer. PMID:31069014
African evolutionary history inferred from whole genome sequence data of 44 indigenous African populations. PMID:31023338
Selective translational usage of TSS and core promoters revealed by translatome sequencing. PMID:30987607
Promoter-Intrinsic and Local Chromatin Features Determine Gene Repression in LADs. PMID:30982597
The Pediatric Cell Atlas: Defining the Growth Phase of Human Development at Single-Cell Resolution. PMID:30930166
Hexosamine Biosynthetic Pathway and Glycosylation Regulate Cell Migration in Melanoma Cells. PMID:30891426
Cellular response to small molecules that selectively stall protein synthesis by the ribosome. PMID:30875366
Displacement of WDR5 from Chromatin by a WIN Site Inhibitor with Picomolar Affinity. PMID:30865883
Shortage of Cellular ATP as a Cause of Diseases and Strategies to Enhance ATP. PMID:30837873
Genetic variants differentially associated with rheumatoid arthritis and systemic lupus erythematosus reveal the disease-specific biology. PMID:30804378
CpG traffic lights are markers of regulatory regions in human genome. PMID:30709331
Discovery of gene regulatory elements through a new bioinformatics analysis of haploid genetic screens. PMID:30695034
RAEdb: a database of enhancers identified by high-throughput reporter assays. PMID:30624654
Antisense Transcription in Loci Associated to Hereditary Neurodegenerative Diseases. PMID:30610612
The Identification and Interpretation of cis-Regulatory Noncoding Mutations in Cancer. PMID:30577431
Dichotomy in redundant enhancers points to presence of initiators of gene regulation. PMID:30563465
Assembly of a parts list of the human mitotic cell cycle machinery. PMID:30452682
Update of the FANTOM web resource: expansion to provide additional transcriptome atlases. PMID:30407557
The UCSC Genome Browser database: 2019 update. PMID:30407534
Multivalent activation of GLP-1 and sulfonylurea receptors modulates β-cell second-messenger signaling and insulin secretion. PMID:30404557
Methylome of human skeletal muscle after acute & chronic resistance exercise training, detraining & retraining. PMID:30375987
A neural network based model effectively predicts enhancers from clinical ATAC-seq samples. PMID:30375457
Lipoteichoic acid anchor triggers Mincle to drive protective immunity against invasive group A Streptococcus infection. PMID:30352847
Tissue-specific pathways and networks underlying sexual dimorphism in non-alcoholic fatty liver disease. PMID:30343673
Comprehensive analysis of long noncoding RNA expression in dorsal root ganglion reveals cell-type specificity and dysregulation after nerve injury. PMID:30335683
Methylation deregulation of miRNA promoters identifies miR124-2 as a survival biomarker in Breast Cancer in very young women. PMID:30258192
De novo pattern discovery enables robust assessment of functional consequences of non-coding variants. PMID:30256891
Genome-wide analysis of DNA methylation in buccal cells: a study of monozygotic twins and mQTLs. PMID:30253792
HACER: an atlas of human active enhancers to interpret regulatory variants. PMID:30247654
An evaluation of supervised methods for identifying differentially methylated regions in Illumina methylation arrays. PMID:30239597
Transcriptional fates of human-specific segmental duplications in brain. PMID:30228200
IQSEC2-related encephalopathy in males and females: a comparative study including 37 novel patients. PMID:30206421
A Computational Method for Classifying Different Human Tissues with Quantitatively Tissue-Specific Expressed Genes. PMID:30205473
Identification of chronological and photoageing-associated microRNAs in human skin. PMID:30154427
Human cardiac cis-regulatory elements, their cognate transcription factors, and regulatory DNA sequence variants. PMID:30139769
Nascent RNA sequencing analysis provides insights into enhancer-mediated gene regulation. PMID:30139328
Conserved temporal ordering of promoter activation implicates common mechanisms governing the immediate early response across cell types and stimuli. PMID:30089658
Bromodomain and extra-terminal domain inhibition modulates the expression of pathologically relevant microRNAs in diffuse large B-cell lymphoma. PMID:30076183
Familial Cancer Variant Prioritization Pipeline version 2 (FCVPPv2) applied to a papillary thyroid cancer family. PMID:30072699
Transcriptional signature primes human oral mucosa for rapid wound healing. PMID:30045979
The STK35 locus contributes to normal gametogenesis and encodes a lncRNA responsive to oxidative stress. PMID:29970477
A fine-mapping study of central obesity loci incorporating functional annotation and imputation. PMID:29967334
CpG island composition differences are a source of gene expression noise indicative of promoter responsiveness. PMID:29945659
Unsupervised clustering and epigenetic classification of single cells. PMID:29925875
Genome-wide association study in Japanese females identifies fifteen novel skin-related trait associations. PMID:29895819
Regulatory variants: from detection to predicting impact. PMID:29893792
Computational approaches for predicting key transcription factors in targeted cell reprogramming (Review). PMID:29845286
GIANT 2.0: genome-scale integrated analysis of gene networks in tissues. PMID:29800226
Towards a map of cis-regulatory sequences in the human genome. PMID:29733395
A Mixed-Effects Model for Powerful Association Tests in Integrative Functional Genomics. PMID:29727690
Palladin Is a Neuron-Specific Translational Target of mTOR Signaling That Regulates Axon Morphogenesis. PMID:29712777
A new approach to epigenome-wide discovery of non-invasive methylation biomarkers for colorectal cancer screening in circulating cell-free DNA using pooled samples. PMID:29686738
NKX2-5 regulates human cardiomyogenesis via a HEY2 dependent transcriptional network. PMID:29636455
Mammalian genomic regulatory regions predicted by utilizing human genomics, transcriptomics, and epigenetics data. PMID:29618048
Peripubertal serum dioxin concentrations and subsequent sperm methylome profiles of young Russian adults. PMID:29550351
Quantifying tumor-infiltrating immune cells from transcriptomics data. PMID:29541787
Effects of Cadmium Exposure on DNA Methylation at Imprinting Control Regions and Genome-Wide in Mothers and Newborn Children. PMID:29529597
Characterization of the human RFX transcription factor family by regulatory and target gene analysis. PMID:29510665
Unravelling the molecular basis for regulatory T-cell plasticity and loss of function in disease. PMID:29497530
Somatic mutagenesis in satellite cells associates with human skeletal muscle aging. PMID:29476074
Identifying noncoding risk variants using disease-relevant gene regulatory networks. PMID:29453388
Identification of novel hyper- or hypomethylated CpG sites and genes associated with atherosclerotic plaque using an epigenome-wide association study. PMID:29436575
GM1 ganglioside-independent intoxication by Cholera toxin. PMID:29432456
Stratification of TAD boundaries reveals preferential insulation of super-enhancers by strong boundaries. PMID:29416042
Region-Specific Methylation Profiling in Acute Myeloid Leukemia. PMID:29405013
ASK Family Kinases Are Required for Optimal NLRP3 Inflammasome Priming. PMID:29353059
Enhancer-associated long non-coding RNA LEENE regulates endothelial nitric oxide synthase and endothelial function. PMID:29348663
Genome-wide association study of self-reported food reactions in Japanese identifies shrimp and peach specific loci in the HLA-DR/DQ gene region. PMID:29348432
GIGGLE: a search engine for large-scale integrated genome analysis. PMID:29309061
PIVOT: platform for interactive analysis and visualization of transcriptomics data. PMID:29304726
KLF1 directly activates expression of the novel fetal globin repressor ZBTB7A/LRF in erythroid cells. PMID:29296711
Principles and methods of in-silico prioritization of non-coding regulatory variants. PMID:29288389
Deciphering the Relationship between Obesity and Various Diseases from a Network Perspective. PMID:29258237
DNA methylation regulates discrimination of enhancers from promoters through a H3K4me1-H3K4me3 seesaw mechanism. PMID:29233090
RetrogeneDB-a database of plant and animal retrocopies. PMID:29220443
Differential Expression of Sox11 and Bdnf mRNA Isoforms in the Injured and Regenerating Nervous Systems. PMID:29209164
Choice of surrogate tissue influences neonatal EWAS findings. PMID:29202839
RATA: A method for high-throughput identification of RNA bound transcription factors. PMID:29201933
Long Non-Coding RNAs in Metabolic Organs and Energy Homeostasis. PMID:29189723
Monitoring transcription initiation activities in rat and dog. PMID:29182598
xCell: digitally portraying the tissue cellular heterogeneity landscape. PMID:29141660
Genome-wide Association Study of Idiopathic Osteonecrosis of the Femoral Head. PMID:29118346
The genetics of obstructive sleep apnoea. PMID:29113020
Deconvolution of Transcriptional Networks in Post-Traumatic Stress Disorder Uncovers Master Regulators Driving Innate Immune System Function. PMID:29101382
MGA repository: a curated data resource for ChIP-seq and other genome annotated data. PMID:29069466
DiseaseEnhancer: a resource of human disease-associated enhancer catalog. PMID:29059320
Timing and localization of human dystrophin isoform expression provide insights into the cognitive phenotype of Duchenne muscular dystrophy. PMID:28974727
Analysis of primary microRNA loci from nascent transcriptomes reveals regulatory domains governed by chromatin architecture. PMID:28973462
Linking FANTOM5 CAGE peaks to annotations with CAGEscan. PMID:28972578
A high resolution atlas of gene expression in the domestic sheep (Ovis aries). PMID:28915238
Systematic analysis of transcription start sites in avian development. PMID:28873399
RefEx, a reference gene expression dataset as a web tool for the functional analysis of genes. PMID:28850115
The FANTOM5 collection, a data series underpinning mammalian transcriptome atlases in diverse cell types. PMID:28850107
FANTOM5 CAGE profiles of human and mouse samples. PMID:28850106
FANTOM5 CAGE profiles of human and mouse reprocessed for GRCh38 and GRCm38 genome assemblies. PMID:28850105
An integrated expression atlas of miRNAs and their promoters in human and mouse. PMID:28829439
Epigenome Aberrations: Emerging Driving Factors of the Clear Cell Renal Cell Carcinoma. PMID:28812986
Genome-wide screen for differentially methylated long noncoding RNAs identifies Esrp2 and lncRNA Esrp2-as regulated by enhancer DNA methylation with prognostic relevance for human breast cancer. PMID:28759043
Novel promoters and coding first exons in DLG2 linked to developmental disorders and intellectual disability. PMID:28724449
Identification and characterization of a FOXA2-regulated transcriptional enhancer at a type 2 diabetes intronic locus that controls GCKR expression in liver cells. PMID:28683826
CpG promoter methylation of the ALKBH3 alkylation repair gene in breast cancer. PMID:28679371
Relevance of tissue specific subunit expression in channelopathies. PMID:28669898
Leucine Differentially Regulates Gene-Specific Translation in Mouse Skeletal Muscle. PMID:28615380
Hierarchical probabilistic models for multiple gene/variant associations based on next-generation sequencing data. PMID:28575251
Comprehensive evaluation of disease- and trait-specific enrichment for eight functional elements among GWAS-identified variants. PMID:28567521
Identification of active miRNA promoters from nuclear run-on RNA sequencing. PMID:28460090
VEXOR: an integrative environment for prioritization of functional variants in fine-mapping analysis. PMID:28453673
DNA methylation: an epigenetic mark of cellular memory. PMID:28450738
De novo RNA sequence assembly during in vivo inflammatory stress reveals hundreds of unannotated lincRNAs in human blood CD14+ monocytes and in adipose tissue. PMID:28389524
Novel RNA biomarkers of prostate cancer revealed by RNA-seq analysis of formalin-fixed samples obtained from Russian patients. PMID:28380430
Transient and permanent changes in DNA methylation patterns in inorganic arsenic-mediated epithelial-to-mesenchymal transition. PMID:28336213
Mutations in INPP5K Cause a Form of Congenital Muscular Dystrophy Overlapping Marinesco-Sjögren Syndrome and Dystroglycanopathy. PMID:28190459
Genome-wide Regional Heritability Mapping Identifies a Locus Within the TOX2 Gene Associated With Major Depressive Disorder. PMID:28153336
Application of hairless mouse strain to bioluminescence imaging of Arc expression in mouse brain. PMID:28114886
Confirmation of five novel susceptibility loci for systemic lupus erythematosus (SLE) and integrated network analysis of 82 SLE susceptibility loci. PMID:28108556
On-the-fly selection of cell-specific enhancers, genes, miRNAs and proteins across the human body using SlideBase. PMID:28025337
The epigenetic landscape of renal cancer. PMID:27890923
Patterns of ribosomal protein expression specify normal and malignant human cells. PMID:27884178
Transcriptional Dynamics During Human Adipogenesis and Its Link to Adipose Morphology and Distribution. PMID:27803022
Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals. PMID:27794045
Computational methods for direct cell conversion. PMID:27736295
Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling. PMID:27717381
NDST1 Preferred Promoter Confirmation and Identification of Corresponding Transcriptional Inhibitors as Substrate Reduction Agents for Multiple Mucopolysaccharidosis Disorders. PMID:27657498
The human PRD-like homeobox gene LEUTX has a central role in embryo genome activation. PMID:27578796
metagene Profiles Analyses Reveal Regulatory Element's Factor-Specific Recruitment Patterns. PMID:27538250
RNA damage in biological conflicts and the diversity of responding RNA repair systems. PMID:27536007
Characterization and target genes of nine human PRD-like homeobox domain genes expressed exclusively in early embryos. PMID:27412763
FANTOM5 transcriptome catalog of cellular states based on Semantic MediaWiki. PMID:27402679
Leukaemia cell of origin identified by chromatin landscape of bulk tumour cells. PMID:27397025
The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability. PMID:27377652
Precision Modulation of Neurodegenerative Disease-Related Gene Expression in Human iPSC-Derived Neurons. PMID:27341390
CAGEd-oPOSSUM: motif enrichment analysis from CAGE-derived TSSs. PMID:27334471
Trans-ethnic Meta-analysis and Functional Annotation Illuminates the Genetic Architecture of Fasting Glucose and Insulin. PMID:27321945
SCOUP: a probabilistic model based on the Ornstein-Uhlenbeck process to analyze single-cell expression data during differentiation. PMID:27277014
Multiplex enhancer-reporter assays uncover unsophisticated TP53 enhancer logic. PMID:27197205
Parallel computation of genome-scale RNA secondary structure to detect structural constraints on human genome. PMID:27153986
Transposable Elements and Their KRAB-ZFP Controllers Regulate Gene Expression in Adult Tissues. PMID:27003935
Identification of Susceptibility Loci and Genes for Colorectal Cancer Risk. PMID:26965516
Genome-wide Association Study of Platelet Count Identifies Ancestry-Specific Loci in Hispanic/Latino Americans. PMID:26805783
Ensembl 2016. PMID:26687719
A novel long non-coding RNA in the rheumatoid arthritis risk locus TRAF1-C5 influences C5 mRNA levels. PMID:26673966
Validation of a DNA methylation microarray for 850,000 CpG sites of the human genome enriched in enhancer sequences. PMID:26673039
Mapping Mammalian Cell-type-specific Transcriptional Regulatory Networks Using KD-CAGE and ChIP-seq Data in the TC-YIK Cell Line. PMID:26635867
COBRA-Seq: Sensitive and Quantitative Methylome Profiling. PMID:26512698
Impaired atrial natriuretic peptide-mediated lipolysis in obesity. PMID:26499437
Public data and open source tools for multi-assay genomic investigation of disease. PMID:26463000
Genome-wide mapping of promoter-anchored interactions with close to single-enhancer resolution. PMID:26313521
Whole-genome sequencing identifies a novel ABCB7 gene mutation for X-linked congenital cerebellar ataxia in a large family of Mongolian ancestry. PMID:26242992
The BioMart community portal: an innovative alternative to large, centralized data repositories. PMID:25897122 -
Update of the FANTOM web resource: expansion to provide additional transcriptome atlases
PubMed citations: 66.
66 articles citing: Update of the FANTOM web resource: expansion to provide additional transcriptome atlases
Altered differentiation of endometrial mesenchymal stromal fibroblasts is associated with endometriosis susceptibility. PMID:35725766
The genes controlling normal function of citrate and spermine secretion are lost in aggressive prostate cancer and prostate model systems. PMID:35707723
The Ramp Atlas: facilitating tissue and cell-specific ramp sequence analyses through an intuitive web interface. PMID:35664804
New Insights on the Regulatory Gene Network Disturbed in Central Areolar Choroidal Dystrophy-Beyond Classical Gene Candidates. PMID:35656327
microRNA-27b regulates hepatic lipase enzyme LIPC and reduces triglyceride degradation during hepatitis C virus infection. PMID:35483451
Cavβ1 regulates T cell expansion and apoptosis independently of voltage-gated Ca2+ channel function. PMID:35440113
An alternative CYB5A transcript is expressed in aneuploid ALL and enriched in relapse. PMID:35436854
ChIP-Atlas 2021 update: a data-mining suite for exploring epigenomic landscapes by fully integrating ChIP-seq, ATAC-seq and Bisulfite-seq data. PMID:35325188
Mouse genomic and cellular annotations. PMID:35124726
Combined inhibition of XIAP and BCL2 drives maximal therapeutic efficacy in genetically diverse aggressive acute myeloid leukemia. PMID:35121960
Characterization of the COPD alveolar niche using single-cell RNA sequencing. PMID:35078977
Widespread occurrence of hybrid internal-terminal exons in human transcriptomes. PMID:35044812
FoxP3 associates with enhancer-promoter loops to regulate Treg-specific gene expression. PMID:35030035
Long read sequencing reveals novel isoforms and insights into splicing regulation during cell state changes. PMID:35012468
Genomic environments scale the activities of diverse core promoters. PMID:34961747
Large-Scale Tissue Microarray Evaluation Corroborates High Specificity of High-Level Arginase-1 Immunostaining for Hepatocellular Carcinoma. PMID:34943588
Pan-Cancer Analysis Reveals the Signature of TMC Family of Genes as a Promising Biomarker for Prognosis and Immunotherapeutic Response. PMID:34899684
Carboxypeptidase A1 (CPA1) Immunohistochemistry Is Highly Sensitive and Specific for Acinar Cell Carcinoma (ACC) of the Pancreas. PMID:34889867
Updates on Immunotherapy and Immune Landscape in Renal Clear Cell Carcinoma. PMID:34831009
TSSr: an R package for comprehensive analyses of TSS sequencing data. PMID:34805991
Full-length transcript sequencing of human and mouse cerebral cortex identifies widespread isoform diversity and alternative splicing. PMID:34788620
FusionGDB 2.0: fusion gene annotation updates aided by deep learning. PMID:34755868
Systems Analysis Reveals Ageing-Related Perturbations in Retinoids and Sex Hormones in Alzheimer's and Parkinson's Diseases. PMID:34680427
Short single-stranded DNAs with putative non-canonical structures comprise a new class of plasma cell-free DNA. PMID:34649537
FusionAI: Predicting fusion breakpoint from DNA sequence with deep learning. PMID:34646994
Krueppel-Like Factor 4 Expression in Phagocytes Regulates Early Inflammatory Response and Disease Severity in Pneumococcal Pneumonia. PMID:34589087
ReFeaFi: Genome-wide prediction of regulatory elements driving transcription initiation. PMID:34491989
Pattern of placental alkaline phosphatase (PLAP) expression in human tumors: a tissue microarray study on 12,381 tumors. PMID:34363325
Decoding disease: from genomes to networks to phenotypes. PMID:34341555
ChIP-GSM: Inferring active transcription factor modules to predict functional regulatory elements. PMID:34292930
A 12 kb multi-allelic copy number variation encompassing a GC gene enhancer is associated with mastitis resistance in dairy cattle. PMID:34288907
Dissecting immune cell stat regulation network reveals biomarkers to predict ICB therapy responders in melanoma. PMID:34238310
Leveraging three-dimensional chromatin architecture for effective reconstruction of enhancer-target gene regulatory interactions. PMID:34197622
TGM4: an immunogenic prostate-restricted antigen. PMID:34193566
Expression of Cancer Testis Antigens in Tumor-Adjacent Normal Liver Is Associated with Post-Resection Recurrence of Hepatocellular Carcinoma. PMID:34065388
Similarities and Differences in Gene Expression Networks Between the Breast Cancer Cell Line Michigan Cancer Foundation-7 and Invasive Human Breast Cancer Tissues. PMID:34056582
Single-cell protein activity analysis identifies recurrence-associated renal tumor macrophages. PMID:34019793
Genome-wide analysis of primary microRNA expression using H3K36me3 ChIP-seq data. PMID:33995896
Expression of Human Endogenous Retroviruses in Systemic Lupus Erythematosus: Multiomic Integration With Gene Expression. PMID:33986751
Mesothelin Expression in Human Tumors: A Tissue Microarray Study on 12,679 Tumors. PMID:33917081
Approaches to Identify and Characterise the Post-Transcriptional Roles of lncRNAs in Cancer. PMID:33803328
The Impact of Modern Technologies on Molecular Diagnostic Success Rates, with a Focus on Inherited Retinal Dystrophy and Hearing Loss. PMID:33799353
Conserved DNA sequence features underlie pervasive RNA polymerase pausing. PMID:33788942
Long read, isoform aware sequencing of mouse nucleus accumbens after chronic cocaine treatment. PMID:33762610
A 44-kb deleted-type copy number variation is associated with decreasing complement component activity and calf mortality in Japanese Black cattle. PMID:33549039
Genome-to-phenome research in rats: progress and perspectives. PMID:33390838
Functional non-coding RNAs in vascular diseases. PMID:33340430
GTRD: an integrated view of transcription regulation. PMID:33231677
Therapeutic potential of miRNAs targeting SARS-CoV-2 host cell receptor ACE2. PMID:33224734
FANTOM enters 20th year: expansion of transcriptomic atlases and functional annotation of non-coding RNAs. PMID:33211864
Analysis of splice variants of the human protein disulfide isomerase (P4HB) gene. PMID:33148170
HeRA: an atlas of enhancer RNAs across human tissues. PMID:33119754
Metabolic recovery after weight loss surgery is reflected in serum microRNAs. PMID:33115818
Single-cell RNA cap and tail sequencing (scRCAT-seq) reveals subtype-specific isoforms differing in transcript demarcation. PMID:33051455
ATP-Binding and Hydrolysis in Inflammasome Activation. PMID:33036374
Renin Angiotensin System, COVID-19 and Male Fertility: Any Risk for Conceiving? PMID:32998451
Stable gene expression for normalisation and single-sample scoring. PMID:32997146
Integrated regulatory models for inference of subtype-specific susceptibilities in glioblastoma. PMID:32974985
Identification of epigenetic interactions between microRNA and DNA methylation associated with polycystic ovarian syndrome. PMID:32759991
Genome-wide association study in a Korean population identifies six novel susceptibility loci for rheumatoid arthritis. PMID:32723749
A comprehensive investigation of the mRNA and protein level of ACE2, the putative receptor of SARS-CoV-2, in human tissues and blood cells. PMID:32669955
Integrated analysis of miRNAs and DNA methylation identifies miR-132-3p as a tumor suppressor in lung adenocarcinoma. PMID:32500672
Molecular networks in Network Medicine: Development and applications. PMID:32307915
Transcriptional control by enhancers and enhancer RNAs. PMID:31791217
Characterization of novel primary miRNA transcription units in human cells using Bru-seq nascent RNA sequencing. PMID:31709421
MicroRNA-27a/b-3p and PPARG regulate SCAMP3 through a feed-forward loop during adipogenesis. PMID:31554889 -
Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation
PubMed citations: 26.
26 articles citing: Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation
Whole-genome sequencing reveals new Alzheimer's disease-associated rare variants in loci related to synaptic function and neuronal development. PMID:33797837
Regulation of miR-1-Mediated Connexin 43 Expression and Cell Proliferation in Dental Epithelial Cells. PMID:32258035
A MicroRNA Network Controls Legionella pneumophila Replication in Human Macrophages via LGALS8 and MX1. PMID:32209695
Benchmark and integration of resources for the estimation of human transcription factor activities. PMID:31340985
Analysis of impact metrics for the Protein Data Bank. PMID:30325351
Neat-en-ing up our understanding of p53 pathways in tumor suppression. PMID:29895201
RCAS: an RNA centric annotation system for transcriptome-wide regions of interest. PMID:28334930
Integration of VDR genome wide binding and GWAS genetic variation data reveals co-occurrence of VDR and NF-κB binding that is linked to immune phenotypes. PMID:28166722
The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes. PMID:28053160
Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals. PMID:27794045
Systematic analysis of the PTEN 5' leader identifies a major AUU initiated proteoform. PMID:27249819
Evolution of the unspliced transcriptome. PMID:26289325
Short stories on zebrafish long noncoding RNAs. PMID:25110965
5meCpG epigenetic marks neighboring a primate-conserved core promoter short tandem repeat indicate X-chromosome inactivation. PMID:25078280
Characteristic bimodal profiles of RNA polymerase II at thousands of active mammalian promoters. PMID:24972996
Dissecting the chromatin interactome of microRNA genes. PMID:24357409
Functional transcriptomics in the post-ENCODE era. PMID:24172201
Identification and characterization of long non-coding RNAs related to mouse embryonic brain development from available transcriptomic data. PMID:23967161
MicroRNA-144 is regulated by activator protein-1 (AP-1) and decreases expression of Alzheimer disease-related a disintegrin and metalloprotease 10 (ADAM10). PMID:23546882
Genome-wide analysis of LXRα activation reveals new transcriptional networks in human atherosclerotic foam cells. PMID:23393188
SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates. PMID:23180783
Strategies to identify long noncoding RNAs involved in gene regulation. PMID:23126680
The plausible reason why the length of 5' untranslated region is unrelated to organismal complexity. PMID:21871111
Semantic-JSON: a lightweight web service interface for Semantic Web contents integrating multiple life science databases. PMID:21632604
microRNA-29 can regulate expression of the long non-coding RNA gene MEG3 in hepatocellular cancer. PMID:21625215
The RIKEN integrated database of mammals. PMID:21076152 -
FANTOM DB: database of Functional Annotation of RIKEN Mouse cDNA Clones
PubMed citations: 25.
25 articles citing: FANTOM DB: database of Functional Annotation of RIKEN Mouse cDNA Clones
Systems Biology to Understand and Regulate Human Retroviral Proinflammatory Response. PMID:34867957
Revisiting the Characteristics of Testicular Germ Cell Lines GC-1(spg) and GC-2(spd)ts. PMID:34125394
mTORC1 activation in lung mesenchyme drives sex- and age-dependent pulmonary structure and function decline. PMID:33159078
Integrating Epigenomics into the Understanding of Biomedical Insight. PMID:27980397
Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals. PMID:27794045
Investigating long noncoding RNAs using animal models. PMID:27479747
Construction of an integrative regulatory element and variation map of the murine Tst locus. PMID:27287690
LncRNA-HIT Functions as an Epigenetic Regulator of Chondrogenesis through Its Recruitment of p100/CBP Complexes. PMID:26633036
Short toxin-like proteins attack the defense line of innate immunity. PMID:23881252
GPMiner: an integrated system for mining combinatorial cis-regulatory elements in mammalian gene group. PMID:22369687
Comparative EST transcript profiling of peach fruits under different post-harvest conditions reveals candidate genes associated with peach fruit quality. PMID:19744325
Genomic landscape of developing male germ cells. PMID:19306351
Cortactin adopts a globular conformation and bundles actin into sheets. PMID:18375393
Computational approaches to phenotyping: high-throughput phenomics. PMID:17202287
Solution structure of the kinase-associated domain 1 of mouse microtubule-associated protein/microtubule affinity-regulating kinase 3. PMID:17075132
Telencephalic embryonic subtractive sequences: a unique collection of neurodevelopmental genes. PMID:16107646
TargetIdentifier: a webserver for identifying full-length cDNAs from EST sequences. PMID:15980559
Comparative promoter region analysis powered by CORG. PMID:15723697
Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PMID:15103394
EICO (Expression-based Imprint Candidate Organizer): finding disease-related imprinted genes. PMID:14681478
Automated Gene Ontology annotation for anonymous sequence data. PMID:12824400
G protein-coupled receptor genes in the FANTOM2 database. PMID:12819145
Comparative analysis of apoptosis and inflammation genes of mice and humans. PMID:12819136
A computer-based method of selecting clones for a full-length cDNA project: simultaneous collection of negligibly redundant and variant cDNAs. PMID:12097351
The Mouse Genome Database (MGD): the model organism database for the laboratory mouse. PMID:11752269 - https://doi.org/10.1093/nar/gkaa1054
Tags:
Tags
More detailed information about this field from each metasource.
cap analysis gene expression
metasource: Fairsharing.org
version: None
genome
metasource: Fairsharing.org
version: None
genome annotation
metasource: Fairsharing.org
version: None
genome visualization
metasource: Fairsharing.org
version: None
micro rna
metasource: Fairsharing.org
version: None
human and other vertebrate genomes
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
human orfs
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
bioinformatic analysis
metasource: re3data.org
version: re3data.org: FANTOM; editing status 2021-10-04; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3JG8M last accessed: 2022-11-04
cdna
metasource: re3data.org
version: re3data.org: FANTOM; editing status 2021-10-04; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3JG8M last accessed: 2022-11-04
cell isolation
metasource: re3data.org
version: re3data.org: FANTOM; editing status 2021-10-04; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3JG8M last accessed: 2022-11-04
chromosome
metasource: re3data.org
version: re3data.org: FANTOM; editing status 2021-10-04; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3JG8M last accessed: 2022-11-04
developmental biology
metasource: re3data.org
version: re3data.org: FANTOM; editing status 2021-10-04; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3JG8M last accessed: 2022-11-04
human cell type
metasource: re3data.org
version: re3data.org: FANTOM; editing status 2021-10-04; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3JG8M last accessed: 2022-11-04
medical genomics
metasource: re3data.org
version: re3data.org: FANTOM; editing status 2021-10-04; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3JG8M last accessed: 2022-11-04
transcription factors and regulatory sites
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:05.943295
gene expression
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:05.943295
gene transcripts
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:05.943295
epigenetics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:05.943295
chip-on-chip
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:05.943295
Tags
More detailed information about this field from each metasource.
cap analysis gene expression
metasource: Fairsharing.orgversion: None
genome
metasource: Fairsharing.orgversion: None
genome annotation
metasource: Fairsharing.orgversion: None
genome visualization
metasource: Fairsharing.orgversion: None
micro rna
metasource: Fairsharing.orgversion: None
human and other vertebrate genomes
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
human orfs
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
bioinformatic analysis
metasource: re3data.orgversion: re3data.org: FANTOM; editing status 2021-10-04; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3JG8M last accessed: 2022-11-04
cdna
metasource: re3data.orgversion: re3data.org: FANTOM; editing status 2021-10-04; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3JG8M last accessed: 2022-11-04
cell isolation
metasource: re3data.orgversion: re3data.org: FANTOM; editing status 2021-10-04; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3JG8M last accessed: 2022-11-04
chromosome
metasource: re3data.orgversion: re3data.org: FANTOM; editing status 2021-10-04; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3JG8M last accessed: 2022-11-04
developmental biology
metasource: re3data.orgversion: re3data.org: FANTOM; editing status 2021-10-04; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3JG8M last accessed: 2022-11-04
human cell type
metasource: re3data.orgversion: re3data.org: FANTOM; editing status 2021-10-04; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3JG8M last accessed: 2022-11-04
medical genomics
metasource: re3data.orgversion: re3data.org: FANTOM; editing status 2021-10-04; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3JG8M last accessed: 2022-11-04
transcription factors and regulatory sites
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:05.943295
gene expression
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:05.943295
gene transcripts
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:05.943295
epigenetics
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:05.943295
chip-on-chip
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:05.943295
cap analysis gene expression genome genome annotation genome visualization micro rna human and other vertebrate genomes human orfs bioinformatic analysis cdna cell isolation chromosome developmental biology human cell type medical genomics transcription factors and regulatory sites gene expression gene transcripts epigenetics chip-on-chip
Need help integrating and/or managing biomedical data?