PAZAR
Names
More detailed information about this field from each metasource.
PAZAR
metasource: Fairsharing.org
version: FAIRsharing.org: PAZAR; PAZAR; DOI: https://doi.org/10.25504/FAIRsharing.33yggg; Last edited: Jan. 8, 2019, 1:19 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:54.111370
pazar
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:54.111370
Names
More detailed information about this field from each metasource.
PAZAR
metasource: Fairsharing.orgversion: FAIRsharing.org: PAZAR; PAZAR; DOI: https://doi.org/10.25504/FAIRsharing.33yggg; Last edited: Jan. 8, 2019, 1:19 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:54.111370
pazar
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:26:54.111370
Names
More detailed information about this field from each metasource.
PAZAR
metasource: Fairsharing.orgversion: FAIRsharing.org: PAZAR; PAZAR; DOI: https://doi.org/10.25504/FAIRsharing.33yggg; Last edited: Jan. 8, 2019, 1:19 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:54.111370
pazar
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:26:54.111370
This source may no longer be available. No known URL could be resolved successfully.
PAZAR is a software framework for the construction and maintenance of regulatory sequence data annotations; a framework which allows multiple boutique databases to function independently within a larger system (or information mall). The goal of PAZAR is to be the public repository for regulatory data.
Description
More detailed information about this field from each metasource.
PAZAR is a software framework for the construction and maintenance of regulatory sequence data annotations; a framework which allows multiple boutique databases to function independently within a larger system (or information mall). The goal of PAZAR is to be the public repository for regulatory data.
metasource: Fairsharing.orgversion: FAIRsharing.org: PAZAR; PAZAR; DOI: https://doi.org/10.25504/FAIRsharing.33yggg; Last edited: Jan. 8, 2019, 1:19 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
Transcription factors and regulatory sequence annotations
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Open access and open source database of transcription factor and regulatory sequence annotation with associated web interface and programming tools designed to submit and query data related to the regulation of gene expression.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:26:54.111370
Webpage:
http://www.pazar.info/Webpage
More detailed information about this field from each metasource.
http://www.pazar.info/
metasource: Fairsharing.orgversion: FAIRsharing.org: PAZAR; PAZAR; DOI: https://doi.org/10.25504/FAIRsharing.33yggg; Last edited: Jan. 8, 2019, 1:19 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:54.111370
Publications:
Publications
More detailed information about this field from each metasource.
The PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences
PMID: 18971253
metasource: Fairsharing.org
version: FAIRsharing.org: PAZAR; PAZAR; DOI: https://doi.org/10.25504/FAIRsharing.33yggg; Last edited: Jan. 8, 2019, 1:19 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
PAZAR: a framework for collection and dissemination of cis-regulatory sequence annotation
PMID: 17916232
metasource: Fairsharing.org
version: FAIRsharing.org: PAZAR; PAZAR; DOI: https://doi.org/10.25504/FAIRsharing.33yggg; Last edited: Jan. 8, 2019, 1:19 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:54.111370
Publications
More detailed information about this field from each metasource.
The PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences
PMID: 18971253
metasource: Fairsharing.org
version: FAIRsharing.org: PAZAR; PAZAR; DOI: https://doi.org/10.25504/FAIRsharing.33yggg; Last edited: Jan. 8, 2019, 1:19 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
PAZAR: a framework for collection and dissemination of cis-regulatory sequence annotation
PMID: 17916232
metasource: Fairsharing.org
version: FAIRsharing.org: PAZAR; PAZAR; DOI: https://doi.org/10.25504/FAIRsharing.33yggg; Last edited: Jan. 8, 2019, 1:19 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:54.111370
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The PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences
PubMed citations: 55.
55 articles citing: The PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences
MYC dosage compensation is mediated by miRNA-transcription factor interactions in aneuploid cancer. PMID:34877484
PKM2-dependent metabolic skewing of hepatic Th17 cells regulates pathogenesis of non-alcoholic fatty liver disease. PMID:34004162
Type I interferon sensing unlocks dormant adipocyte inflammatory potential. PMID:32488081
Clinical implications of chromatin accessibility in human cancers. PMID:32405341
Benchmark and integration of resources for the estimation of human transcription factor activities. PMID:31340985
Integration of Multiple Data Sources for Gene Network Inference Using Genetic Perturbation Data. PMID:31009236
An Exploration Into Improving DNA Motif Inference by Looking for Highly Conserved Core Regions. PMID:31008453
Defective transcription elongation in a subset of cancers confers immunotherapy resistance. PMID:30353012
Diesel exhaust and house dust mite allergen lead to common changes in the airway methylome and hydroxymethylome. PMID:30090644
Agrin has a pathological role in the progression of oral cancer. PMID:29872149
Involvement of MAFB and MAFF in Retinoid-Mediated Suppression of Hepatocellular Carcinoma Invasion. PMID:29757260
Nasal DNA methylation is associated with childhood asthma. PMID:29692198
Transcription factors operate across disease loci, with EBNA2 implicated in autoimmunity. PMID:29662164
Systematic target function annotation of human transcription factors. PMID:29325558
A causal mediation model of ischemia reperfusion injury in the retina. PMID:29121052
SalmoNet, an integrated network of ten Salmonella enterica strains reveals common and distinct pathways to host adaptation. PMID:29057095
HTS-Net: An integrated regulome-interactome approach for establishing network regulation models in high-throughput screenings. PMID:28949986
Temporal, spatial, and phenotypical changes of PDGFRα expressing fibroblasts during late lung development. PMID:28408205
Identification of critical paralog groups with indispensable roles in the regulation of signaling flow. PMID:27922122
Interactive cooperation and hierarchical operation of microRNA and transcription factor crosstalk in human transcriptional regulatory network. PMID:27879476
Evaluating tools for transcription factor binding site prediction. PMID:27806697
ORTI: An Open-Access Repository of Transcriptional Interactions for Interrogating Mammalian Gene Expression Data. PMID:27723773
PAX6 MiniPromoters drive restricted expression from rAAV in the adult mouse retina. PMID:27556059
ARN: analysis and prediction by adipogenic professional database. PMID:27503118
Systems Genetic Analyses Highlight a TGFβ-FOXO3 Dependent Striatal Astrocyte Network Conserved across Species and Associated with Stress, Sleep, and Huntington's Disease. PMID:27390852
Topoisomerase 1 inhibition suppresses inflammatory genes and protects from death by inflammation. PMID:27127234
Integrative transcriptome analysis identifies deregulated microRNA-transcription factor networks in lung adenocarcinoma. PMID:27081085
Circuits of cancer drivers revealed by convergent misregulation of transcription factor targets across tumor types. PMID:26792175
AURA 2: Empowering discovery of post-transcriptional networks. PMID:26779400
ORegAnno 3.0: a community-driven resource for curated regulatory annotation. PMID:26578589
FARE-CAFE: a database of functional and regulatory elements of cancer-associated fusion events. PMID:26384373
STAT3 pathway regulates lung-derived brain metastasis initiating cell capacity through miR-21 activation. PMID:26314961
Impaired Cell Cycle Regulation in a Natural Equine Model of Asthma. PMID:26292153
Combined serial analysis of gene expression and transcription factor binding site prediction identifies novel-candidate-target genes of Nr2e1 in neocortex development. PMID:26204903
Regulatory networks in retinal ischemia-reperfusion injury. PMID:25902940
A Study into the Evolutionary Divergence of the Core Promoter Elements of PRPF31 and TFPT. PMID:25729402
Autophagy Regulatory Network - a systems-level bioinformatics resource for studying the mechanism and regulation of autophagy. PMID:25635527
Finding gene regulatory network candidates using the gene expression knowledge base. PMID:25490885
Dissecting the causal genetic mechanisms of coronary heart disease. PMID:24623178
JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles. PMID:24194598
The next generation of transcription factor binding site prediction. PMID:24039567
RegTransBase--a database of regulatory sequences and interactions based on literature: a resource for investigating transcriptional regulation in prokaryotes. PMID:23547897
LASAGNA: a novel algorithm for transcription factor binding site alignment. PMID:23522376
A quantitative proteomic profile of the Nrf2-mediated antioxidant response of macrophages to oxidized LDL determined by multiplexed selected reaction monitoring. PMID:23166812
The dependence of expression of NF-κB-dependent genes: statistics and evolutionary conservation of control sequences in the promoter and in the 3' UTR. PMID:22577947
The transcription factor encyclopedia. PMID:22458515
Identification of cis-regulatory sequence variations in individual genome sequences. PMID:21989199
Exploring pathway interactions in insulin resistant mouse liver. PMID:21843341
MIR@NT@N: a framework integrating transcription factors, microRNAs and their targets to identify sub-network motifs in a meta-regulation network model. PMID:21375730
Evolution of gene regulation of pluripotency--the case for wiki tracks at genome browsers. PMID:21190561
UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein-DNA interactions. PMID:21037262
A computational evaluation of over-representation of regulatory motifs in the promoter regions of differentially expressed genes. PMID:20487530
Phyloscan: locating transcription-regulating binding sites in mixed aligned and unaligned sequence data. PMID:20435683
Identification and characterization of putative methylation targets in the MAOA locus using bioinformatic approaches. PMID:20421737
JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles. PMID:19906716 -
PAZAR: a framework for collection and dissemination of cis-regulatory sequence annotation
PubMed citations: 55.
55 articles citing: PAZAR: a framework for collection and dissemination of cis-regulatory sequence annotation
Differential gene expression orchestrated by transcription factors in osteoporosis: bioinformatics analysis of associated polymorphism elaborating functional relationships. PMID:35748775
Cas9-mediated genome editing reveals a significant contribution of calcium signaling pathways to anhydrobiosis in Pv11 cells. PMID:34611198
Genome-wide pathogenesis interpretation using a heat diffusion-based systems genetics method and implications for gene function annotation. PMID:32869547
Reprogramming of macrophages employing gene regulatory and metabolic network models. PMID:32097424
Modelling TERT regulation across 19 different cancer types based on the MIPRIP 2.0 gene regulatory network approach. PMID:31888467
PropaNet: Time-Varying Condition-Specific Transcriptional Network Construction by Network Propagation. PMID:31258543
Integration of Multiple Data Sources for Gene Network Inference Using Genetic Perturbation Data. PMID:31009236
Transcriptomic Data Identified Key Transcription Factors for Osteoporosis in Caucasian Women. PMID:30056508
A data-driven, knowledge-based approach to biomarker discovery: application to circulating microRNA markers of colorectal cancer prognosis. PMID:29872543
A causal mediation model of ischemia reperfusion injury in the retina. PMID:29121052
TRRUST v2: an expanded reference database of human and mouse transcriptional regulatory interactions. PMID:29087512
ARN: Analysis and Visualization System for Adipogenic Regulation Network Information. PMID:27982098
ORTI: An Open-Access Repository of Transcriptional Interactions for Interrogating Mammalian Gene Expression Data. PMID:27723773
PAX6 MiniPromoters drive restricted expression from rAAV in the adult mouse retina. PMID:27556059
Transcriptome Alterations In X-Irradiated Human Gingiva Fibroblasts. PMID:27356049
Epigenetic Signatures of Salivary Gland Inflammation in Sjögren's Syndrome. PMID:27332624
Identification of Biomarker and Co-Regulatory Motifs in Lung Adenocarcinoma Based on Differential Interactions. PMID:26402252
Combined serial analysis of gene expression and transcription factor binding site prediction identifies novel-candidate-target genes of Nr2e1 in neocortex development. PMID:26204903
Global transcription network incorporating distal regulator binding reveals selective cooperation of cancer drivers and risk genes. PMID:26001967
Cis-regulatory somatic mutations and gene-expression alteration in B-cell lymphomas. PMID:25903198
Regulatory networks in retinal ischemia-reperfusion injury. PMID:25902940
Systems-level perspective of sudden infant death syndrome. PMID:24964230
Navigating the multilayered organization of eukaryotic signaling: a new trend in data integration. PMID:24550716
RANK- and c-Met-mediated signal network promotes prostate cancer metastatic colonization. PMID:24478054
Functional analysis of microRNA and transcription factor synergistic regulatory network based on identifying regulatory motifs in non-small cell lung cancer. PMID:24200043
JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles. PMID:24194598
The next generation of transcription factor binding site prediction. PMID:24039567
PhysBinder: Improving the prediction of transcription factor binding sites by flexible inclusion of biophysical properties. PMID:23620286
Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review. PMID:23384594
SignaLink 2 - a signaling pathway resource with multi-layered regulatory networks. PMID:23331499
The DNA damage- and transcription-associated protein paxip1 controls thymocyte development and emigration. PMID:23159437
DICER- and AGO3-dependent generation of retinoic acid-induced DR2 Alu RNAs regulates human stem cell proliferation. PMID:23064648
A flexible integrative approach based on random forest improves prediction of transcription factor binding sites. PMID:22492513
The transcription factor encyclopedia. PMID:22458515
Validation of skeletal muscle cis-regulatory module predictions reveals nucleotide composition bias in functional enhancers. PMID:22144875
Identification of cis-regulatory sequence variations in individual genome sequences. PMID:21989199
Towards resolving the transcription factor network controlling myelin gene expression. PMID:21729871
Genome-wide screening in human growth plates during puberty in one patient suggests a role for RUNX2 in epiphyseal maturation. PMID:21307122
Evolution of gene regulation of pluripotency--the case for wiki tracks at genome browsers. PMID:21190561
The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources. PMID:21030441
A regulatory toolbox of MiniPromoters to drive selective expression in the brain. PMID:20807748
Global mapping of binding sites for Nrf2 identifies novel targets in cell survival response through ChIP-Seq profiling and network analysis. PMID:20460467
Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding. PMID:20378774
Transcription factor regulation can be accurately predicted from the presence of target gene signatures in microarray gene expression data. PMID:20215436
Discovery of regulatory elements is improved by a discriminatory approach. PMID:19911049
JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles. PMID:19906716
The PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences. PMID:18971253
UniPROBE: an online database of protein binding microarray data on protein-DNA interactions. PMID:18842628
Identification of a set of genes showing regionally enriched expression in the mouse brain. PMID:18625066
Screening for PPAR Responsive Regulatory Modules in Cancer. PMID:18551184
ConTra: a promoter alignment analysis tool for identification of transcription factor binding sites across species. PMID:18453628
ModuleMiner - improved computational detection of cis-regulatory modules: are there different modes of gene regulation in embryonic development and adult tissues? PMID:18394174
Text-mining assisted regulatory annotation. PMID:18271954
JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update. PMID:18006571
ORegAnno: an open-access community-driven resource for regulatory annotation. PMID:18006570
Tags:
Tags
More detailed information about this field from each metasource.
biological regulation
metasource: Fairsharing.org
version: FAIRsharing.org: PAZAR; PAZAR; DOI: https://doi.org/10.25504/FAIRsharing.33yggg; Last edited: Jan. 8, 2019, 1:19 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
deoxyribonucleic acid
metasource: Fairsharing.org
version: FAIRsharing.org: PAZAR; PAZAR; DOI: https://doi.org/10.25504/FAIRsharing.33yggg; Last edited: Jan. 8, 2019, 1:19 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
regulation of gene expression
metasource: Fairsharing.org
version: FAIRsharing.org: PAZAR; PAZAR; DOI: https://doi.org/10.25504/FAIRsharing.33yggg; Last edited: Jan. 8, 2019, 1:19 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
ribonucleic acid
metasource: Fairsharing.org
version: FAIRsharing.org: PAZAR; PAZAR; DOI: https://doi.org/10.25504/FAIRsharing.33yggg; Last edited: Jan. 8, 2019, 1:19 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
transcription factor
metasource: Fairsharing.org
version: FAIRsharing.org: PAZAR; PAZAR; DOI: https://doi.org/10.25504/FAIRsharing.33yggg; Last edited: Jan. 8, 2019, 1:19 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
nucleotide sequence databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
transcriptional regulator sites and transcription factors
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
transcription factors and regulatory sites
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:54.111370
gene expression
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:54.111370
gene regulation
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:54.111370
gene transcripts
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:54.111370
Tags
More detailed information about this field from each metasource.
biological regulation
metasource: Fairsharing.orgversion: FAIRsharing.org: PAZAR; PAZAR; DOI: https://doi.org/10.25504/FAIRsharing.33yggg; Last edited: Jan. 8, 2019, 1:19 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
deoxyribonucleic acid
metasource: Fairsharing.orgversion: FAIRsharing.org: PAZAR; PAZAR; DOI: https://doi.org/10.25504/FAIRsharing.33yggg; Last edited: Jan. 8, 2019, 1:19 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
regulation of gene expression
metasource: Fairsharing.orgversion: FAIRsharing.org: PAZAR; PAZAR; DOI: https://doi.org/10.25504/FAIRsharing.33yggg; Last edited: Jan. 8, 2019, 1:19 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
ribonucleic acid
metasource: Fairsharing.orgversion: FAIRsharing.org: PAZAR; PAZAR; DOI: https://doi.org/10.25504/FAIRsharing.33yggg; Last edited: Jan. 8, 2019, 1:19 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
transcription factor
metasource: Fairsharing.orgversion: FAIRsharing.org: PAZAR; PAZAR; DOI: https://doi.org/10.25504/FAIRsharing.33yggg; Last edited: Jan. 8, 2019, 1:19 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
nucleotide sequence databases
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
transcriptional regulator sites and transcription factors
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
transcription factors and regulatory sites
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:26:54.111370
gene expression
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:26:54.111370
gene regulation
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:26:54.111370
gene transcripts
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:26:54.111370
biological regulation dna regulation of gene expression rna transcription nucleic acid sequence transcription transcription factors and regulatory sites gene expression gene regulation gene transcripts
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