Multi Experiment Matrix (MEM)
MEM (Multi-Experiment Matrix) provides gene expression similarity searches, visualisation and analyses across many datasets from ArrayExpress and GEO. MEM uses rank aggregation to merge information from different datasets into a single global ordering with simultaneous statistical significance estimation. Each dataset can be also accessed through ExpressView gene clustering and visualisation, and DiffExp for differential expressed genes search.
Description
More detailed information about this field from each metasource.
MEM (Multi-Experiment Matrix) provides gene expression similarity searches, visualisation and analyses across many datasets from ArrayExpress and GEO. MEM uses rank aggregation to merge information from different datasets into a single global ordering with simultaneous statistical significance estimation. Each dataset can be also accessed through ExpressView gene clustering and visualisation, and DiffExp for differential expressed genes search.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:31:15.989234
Webpage:
http://biit.cs.ut.ee/mem/Webpage
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Name: FreewareLicence name
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Publications:
Publications
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Mining for coexpression across hundreds of datasets using novel rank aggregation and visualization methods
PMID: 19961599
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:15.989234
Publications
More detailed information about this field from each metasource.
Mining for coexpression across hundreds of datasets using novel rank aggregation and visualization methods
PMID: 19961599
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:15.989234
-
Mining for coexpression across hundreds of datasets using novel rank aggregation and visualization methods
PubMed citations: 86.
86 articles citing: Mining for coexpression across hundreds of datasets using novel rank aggregation and visualization methods
Nomograms combined with SERPINE1-related module genes predict overall and recurrence-free survival after curative resection of gastric cancer: a study based on TCGA and GEO data. PMID:35117805
LINC00261 elevation inhibits angiogenesis and cell cycle progression of pancreatic cancer cells by upregulating SCP2 via targeting FOXP3. PMID:34541823
Reciprocal YAP1 loss and INSM1 expression in neuroendocrine prostate cancer. PMID:34431104
Expression and Clinical Significance of BCL2 Interacting Protein 3 Like in Multiple Myeloma. PMID:34189969
The potential roles of lncRNAs DUXAP8, LINC00963, and FOXD2-AS1 in luminal breast cancer based on expression analysis and bioinformatic approaches. PMID:34043149
Bioinformatics and survival analysis of glia maturation factor-γ in pan-cancers. PMID:33863293
Loss of LIMCH1 predicts poor prognosis in patients with surgically resected Lung Adenocarcinoma: A study based on Immunohistochemical Analysis and Bioinformatics. PMID:33391414
Identification of the 3-lncRNA Signature as a Prognostic Biomarker for Colorectal Cancer. PMID:33302562
Lower expression of LINC00092 in lung adenocarcinoma might mean poorer prognosis: A study based on data mining and bioinformatics. PMID:33126385
Healthspan pathway maps in C. elegans and humans highlight transcription, proliferation/biosynthesis and lipids. PMID:32634117
MiR-101-containing extracellular vesicles bind to BRD4 and enhance proliferation and migration of trophoblasts in preeclampsia. PMID:32527308
Scoring functions for drug-effect similarity. PMID:32484516
Genetic association analysis of CLEC5A and CLEC7A gene single-nucleotide polymorphisms and Crohn's disease. PMID:32476786
An alteration of the dopamine synthetic pathway is possibly involved in the pathophysiology of COVID-19. PMID:32246784
Silencing of ATP2B1-AS1 contributes to protection against myocardial infarction in mouse via blocking NFKBIA-mediated NF-κB signalling pathway. PMID:32155320
The Demonstration of an Aqp4/Tgf-beta 1 Pathway in Murine Astrocytes Holds Implications for Both Neuromyelitis Optica and Progressive Multiple Sclerosis. PMID:32033173
Prediction of overall survival time in patients with colon adenocarcinoma using DNA methylation profiling of long non-coding RNAs. PMID:32002035
Overexpressed lncRNA GATA6-AS1 Inhibits LNM and EMT via FZD4 through the Wnt/β-Catenin Signaling Pathway in GC. PMID:31981860
Long Noncoding RNA LINC00265 Targets EGFR and Promotes Deterioration of Colorectal Cancer: A Comprehensive Study Based on Data Mining and in vitro Validation. PMID:31824175
LINC00460 Hypomethylation Promotes Metastasis in Colorectal Carcinoma. PMID:31632435
Improved gene co-expression network quality through expression dataset down-sampling and network aggregation. PMID:31594989
Overexpressed BSG related to the progression of lung adenocarcinoma with high-throughput data-mining, immunohistochemistry, in vitro validation and in silico investigation. PMID:31497203
Gene Regulatory Networks in Peripheral Mononuclear Cells Reveals Critical Regulatory Modules and Regulators of Multiple Sclerosis. PMID:31484947
Downregulated long non-coding RNA LINC00899 inhibits invasion and migration of spinal ependymoma cells via RBL2-dependent FoxO pathway. PMID:31432742
HENA, heterogeneous network-based data set for Alzheimer's disease. PMID:31413325
A liver-specific lncRNA, FAM99B, suppresses hepatocellular carcinoma progression through inhibition of cell proliferation, migration, and invasion. PMID:31243545
g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update). PMID:31066453
A five lncRNA signature for prognosis prediction in hepatocellular carcinoma. PMID:31059056
Long non-coding RNA LINC01314 represses cell migration, invasion, and angiogenesis in gastric cancer via the Wnt/β-catenin signaling pathway by down-regulating KLK4. PMID:31007611
Long Non-coding RNA PVT1 Competitively Binds MicroRNA-424-5p to Regulate CARM1 in Radiosensitivity of Non-Small-Cell Lung Cancer. PMID:30861415
YESdb: integrative analysis of environmental stress in yeast. PMID:30821814
Long non-coding RNA LINC00968 attenuates drug resistance of breast cancer cells through inhibiting the Wnt2/β-catenin signaling pathway by regulating WNT2. PMID:30791958
Clinical significance and effect of MTDH/AEG-1 in bladder urothelial cancer: a study based on immunohistochemistry, RNA-seq, and in vitro verification. PMID:30588098
A risk assessment model for the prognosis of osteosarcoma utilizing differentially expressed lncRNAs. PMID:30569146
funcExplorer: a tool for fast data-driven functional characterisation of high-throughput expression data. PMID:30428831
Expression, Clinical Significance, and Functional Prediction of MNX1 in Breast Cancer. PMID:30368216
Downregulation of the long noncoding RNA MBNL1-AS1 protects sevoflurane-pretreated mice against ischemia-reperfusion injury by targeting KCNMA1. PMID:30185781
Capturing functional long non-coding RNAs through integrating large-scale causal relations from gene perturbation experiments. PMID:30177244
Potential role of LINC00996 in colorectal cancer: a study based on data mining and bioinformatics. PMID:30147336
Silencing of Long Noncoding RNA SOX21-AS1 Relieves Neuronal Oxidative Stress Injury in Mice with Alzheimer's Disease by Upregulating FZD3/5 via the Wnt Signaling Pathway. PMID:30143969
Risk assessment model constructed by differentially expressed lncRNAs for the prognosis of glioma. PMID:30106138
Up-regulation of CTD-2547G23.4 in hepatocellular carcinoma tissues and its prospective molecular regulatory mechanism: a novel qRT-PCR and bioinformatics analysis study. PMID:29780284
Identification of a 5‑lncRNA signature‑based risk scoring system for survival prediction in colorectal cancer. PMID:29749517
Long non-coding RNAs RP5-821D11.7, APCDD1L-AS1 and RP11-277P12.9 were associated with the prognosis of lung squamous cell carcinoma. PMID:29568882
Bioinformatics analysis of differentially expressed gene profiles associated with systemic lupus erythematosus. PMID:29257335
Long non-coding RNA polymorphisms in 6p21.1 are associated with atrophic gastritis risk and gastric cancer prognosis. PMID:29221129
Glut3 Addiction Is a Druggable Vulnerability for a Molecularly Defined Subpopulation of Glioblastoma. PMID:29198914
Gene expression signatures of neuroendocrine prostate cancer and primary small cell prostatic carcinoma. PMID:29132337
Prediction of clinical outcome and survival in soft-tissue sarcoma using a ten-lncRNA signature. PMID:29113307
Long non‑coding RNA HOTTIP promotes hepatocellular carcinoma tumorigenesis and development: A comprehensive investigation based on bioinformatics, qRT‑PCR and meta‑analysis of 393 cases. PMID:29039502
Comprehensive analysis of long non-coding RNA PVT1 gene interaction regulatory network in hepatocellular carcinoma using gene microarray and bioinformatics. PMID:28979669
CLIC, a tool for expanding biological pathways based on co-expression across thousands of datasets. PMID:28719601
Clinical Significance and Effect of lncRNA HOXA11-AS in NSCLC: A Study Based on Bioinformatics, In Vitro and in Vivo Verification. PMID:28717185
Study of Meta-analysis strategies for network inference using information-theoretic approaches. PMID:28484519
Detection of lower levels of SNAP25 using multiple microarray systems and its functional significance in medulloblastoma. PMID:28339008
Chromosomal abnormalities and molecular landscape of metastasizing mucinous salivary adenocarcinoma. PMID:28249646
Expression Profiling of Clinical Specimens Supports the Existence of Neural Progenitor-Like Stem Cells in Basal Breast Cancers. PMID:28216417
Comprehensive investigation of a novel differentially expressed lncRNA expression profile signature to assess the survival of patients with colorectal adenocarcinoma. PMID:28187432
Clinical significance and effect of AEG-1 on the proliferation, invasion, and migration of NSCLC: a study based on immunohistochemistry, TCGA, bioinformatics, in vitro and in vivo verification. PMID:28152520
CellMapper: rapid and accurate inference of gene expression in difficult-to-isolate cell types. PMID:27687735
g:Profiler-a web server for functional interpretation of gene lists (2016 update). PMID:27098042
Gene co-expression analysis unravels a link between C9orf72 and RNA metabolism in myeloid cells. PMID:26472214
An interactive web application for the dissemination of human systems immunology data. PMID:26088622
ClustVis: a web tool for visualizing clustering of multivariate data using Principal Component Analysis and heatmap. PMID:25969447
Network tuned multiple rank aggregation and applications to gene ranking. PMID:25708095
Finding genetic overlaps among diseases based on ranked gene lists. PMID:25684200
Targeted exploration and analysis of large cross-platform human transcriptomic compendia. PMID:25581801
Toward computational cumulative biology by combining models of biological datasets. PMID:25427176
yStreX: yeast stress expression database. PMID:25024351
Glycerol-3-phosphate acyltranferase-2 behaves as a cancer testis gene and promotes growth and tumorigenicity of the breast cancer MDA-MB-231 cell line. PMID:24967918
Integration of biological data by kernels on graph nodes allows prediction of new genes involved in mitotic chromosome condensation. PMID:24943848
The CO-Regulation Database (CORD): a tool to identify coordinately expressed genes. PMID:24599084
RIG-I-like receptor LGP2 protects tumor cells from ionizing radiation. PMID:24434553
Human disease locus discovery and mapping to molecular pathways through phylogenetic profiling. PMID:24084807
Identification of signaling pathways modulated by RHBDD2 in breast cancer cells: a link to the unfolded protein response. PMID:24078384
ANTXR1, a stem cell-enriched functional biomarker, connects collagen signaling to cancer stem-like cells and metastasis in breast cancer. PMID:23832666
Diagnostic SOX10 gene signatures in salivary adenoid cystic and breast basal-like carcinomas. PMID:23799842
An integrative approach to inferring gene regulatory module networks. PMID:23285197
Computational selection of transcriptomics experiments improves Guilt-by-Association analyses. PMID:22879875
Systematic identification of functional plant modules through the integration of complementary data sources. PMID:22589469
Robust rank aggregation for gene list integration and meta-analysis. PMID:22247279
Research resource: interactome of human embryo implantation: identification of gene expression pathways, regulation, and integrated regulatory networks. PMID:22074951
Transcriptional gene network inference from a massive dataset elucidates transcriptome organization and gene function. PMID:21785136
g:Profiler--a web server for functional interpretation of gene lists (2011 update). PMID:21646343
ZNF703 gene amplification at 8p12 specifies luminal B breast cancer. PMID:21328542
mRNA expression analysis of cell cycle genes in islets of pregnant mice. PMID:20886204
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gene expression
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:15.989234
microarray experiment
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:15.989234
functional, regulatory and non-coding rna
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:15.989234
molecular interactions, pathways and networks
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:15.989234
data mining
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:15.989234
Tags
More detailed information about this field from each metasource.
gene expression
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:31:15.989234
microarray experiment
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:31:15.989234
functional, regulatory and non-coding rna
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:31:15.989234
molecular interactions, pathways and networks
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:31:15.989234
data mining
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:31:15.989234
gene expression microarray experiment functional, regulatory and non-coding rna molecular interactions, pathways and networks data mining
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