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GSKB: A gene set database for pathway analysis in mouse

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Micro-RNA profiling reveals a role for miR-29 in human and murine liver fibrosis

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Mutations inNR0B1 (DAX1) andNR5A1 (SF1) responsible for adrenal hypoplasia congenita

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The Comparative Toxicogenomics Database (CTD): a resource for comparative toxicological studies

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Absence of an adipogenic effect of rosiglitazone on mature 3T3-L1 adipocytes: increase of lipid catabolism and reduction of adipokine expression

inferredcites →https://doi.org/10.1007/s00335-012-9421-3openalex-snapshot

The Mammalian Phenotype Ontology as a unifying standard for experimental and high-throughput phenotyping data

inferredcites →https://doi.org/10.1016/j.bbrc.2009.11.056openalex-snapshot

Suppression of type I collagen production by microRNA-29b in cultured human stellate cells

inferredcites →https://doi.org/10.1016/j.cytogfr.2005.09.008openalex-snapshot

Smad3 is key to TGF-β-mediated epithelial-to-mesenchymal transition, fibrosis, tumor suppression and metastasis

inferredcites →https://doi.org/10.1016/j.febslet.2009.12.053openalex-snapshot

High glucose down‐regulates miR‐29a to increase collagen IV production in HK‐2 cells

inferredcites →https://doi.org/10.1016/j.fob.2012.04.003openalex-snapshot

GeneSetDB: A comprehensive meta‐database, statistical and visualisation framework for gene set analysis

inferredcites →https://doi.org/10.1016/j.molcel.2007.06.017openalex-snapshot

MicroRNA Targeting Specificity in Mammals: Determinants beyond Seed Pairing

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Up-Regulation of Glial Fibrillary Acidic Protein in Response to Retinal Injury: Its Potential Role in Glial Remodeling and a Comparison to Vimentin Expression

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SREBP-1, a basic-helix-loop-helix-leucine zipper protein that controls transcription of the low density lipoprotein receptor gene

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PPARγ Is Required for the Differentiation of Adipose Tissue In Vivo and In Vitro

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The effects of dietary curcumin and rutin on colonic inflammation and gene expression in multidrug resistance gene-deficient (mdr1a−/−) mice, a model of inflammatory bowel diseases

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Spi-1 is a putative oncogene in virally induced murine erythroleukaemias

inferredcites →https://doi.org/10.1038/75556openalex-snapshot

Gene Ontology: tool for the unification of biology

inferredcites →https://doi.org/10.1038/msb.2009.98openalex-snapshot

A side effect resource to capture phenotypic effects of drugs

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The Edinburgh human metabolic network reconstruction and its functional analysis

inferredcites →https://doi.org/10.1038/mt.2012.36openalex-snapshot

miR-29 Inhibits Bleomycin-induced Pulmonary Fibrosis in Mice

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Hepatocyte nuclear factor 4α controls the development of a hepatic epithelium and liver morphogenesis

inferredcites →https://doi.org/10.1038/ng1318openalex-snapshot

Rb regulates proliferation and rod photoreceptor development in the mouse retina

inferredcites →https://doi.org/10.1038/ng1536openalex-snapshot

Combinatorial microRNA target predictions

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MethCancerDB – aberrant DNA methylation in human cancer

inferredcites →https://doi.org/10.1073/pnas.0506580102openalex-snapshot

Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles

inferredcites →https://doi.org/10.1073/pnas.0805038105openalex-snapshot

Dysregulation of microRNAs after myocardial infarction reveals a role of miR-29 in cardiac fibrosis

inferredcites →https://doi.org/10.1093/bioinformatics/btr260openalex-snapshot

Molecular signatures database (MSigDB) 3.0

inferredcites →https://doi.org/10.1093/bioinformatics/bts421openalex-snapshot

AraPath: a knowledgebase for pathway analysis in Arabidopsis

inferredcites →https://doi.org/10.1093/biostatistics/4.2.249openalex-snapshot

Exploration, normalization, and summaries of high density oligonucleotide array probe level data

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Towards BioDBcore: a community-defined information specification for biological databases

inferredcites →https://doi.org/10.1093/database/bar052openalex-snapshot

INOH: ontology-based highly structured database of signal transduction pathways

inferredcites →https://doi.org/10.1093/nar/28.1.316openalex-snapshot

TRANSFAC: an integrated system for gene expression regulation

inferredcites →https://doi.org/10.1093/nar/gki004openalex-snapshot

TRED: a Transcriptional Regulatory Element Database and a platform for in silico gene regulation studies

inferredcites →https://doi.org/10.1093/nar/gki078openalex-snapshot

The PANTHER database of protein families, subfamilies, functions and pathways

inferredcites →https://doi.org/10.1093/nar/gki418openalex-snapshot

FFAS03: a server for profile-profile sequence alignments

inferredcites →https://doi.org/10.1093/nar/gkj102openalex-snapshot

From genomics to chemical genomics: new developments in KEGG

inferredcites →https://doi.org/10.1093/nar/gkl811openalex-snapshot

CancerGenes: a gene selection resource for cancer genome projects

inferredcites →https://doi.org/10.1093/nar/gkm323openalex-snapshot

GeneTrail--advanced gene set enrichment analysis

inferredcites →https://doi.org/10.1093/nar/gkm730openalex-snapshot

MethyCancer: the database of human DNA methylation and cancer

inferredcites →https://doi.org/10.1093/nar/gkm795openalex-snapshot

STITCH: interaction networks of chemicals and proteins

inferredcites →https://doi.org/10.1093/nar/gkm862openalex-snapshot

SuperTarget and Matador: resources for exploring drug-target relationships

inferredcites →https://doi.org/10.1093/nar/gkm958openalex-snapshot

DrugBank: a knowledgebase for drugs, drug actions and drug targets

inferredcites →https://doi.org/10.1093/nar/gkm995openalex-snapshot

The microRNA.org resource: targets and expression

inferredcites →https://doi.org/10.1093/nar/gkn653openalex-snapshot

PID: The Pathway Interaction Database

inferredcites →https://doi.org/10.1093/nar/gkn923openalex-snapshot

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

inferredcites →https://doi.org/10.1093/nar/gkp1002openalex-snapshot

SMPDB: The Small Molecule Pathway Database

inferredcites →https://doi.org/10.1093/nar/gkp934openalex-snapshot

T3DB: a comprehensively annotated database of common toxins and their targets

inferredcites →https://doi.org/10.1093/nar/gkq1107openalex-snapshot

miRTarBase: a database curates experimentally validated microRNA–target interactions

inferredcites →https://doi.org/10.1093/nar/gkq149openalex-snapshot

Transcription factor regulation can be accurately predicted from the presence of target gene signatures in microarray gene expression data

inferredcites →https://doi.org/10.1093/nar/gkr1074openalex-snapshot

WikiPathways: building research communities on biological pathways

inferredcites →https://doi.org/10.1093/nar/gkr1161openalex-snapshot

TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support

inferredcites →https://doi.org/10.1093/nar/gkr901openalex-snapshot

GeneSigDB: a manually curated database and resource for analysis of gene expression signatures

inferredcites →https://doi.org/10.1093/nar/gni105openalex-snapshot

Improved microarray methods for profiling the yeast knockout strain collection

inferredcites →https://doi.org/10.1096/fj.06-6211comopenalex-snapshot

Biological characterization of gene response in Rpe65‐/‐ mouse model of Leber's congenital amaurosis during progression of the disease

inferredcites →https://doi.org/10.1097/mpg.0b013e318244148bopenalex-snapshot

MicroRNA Profiling Identifies miR‐29 as a Regulator of Disease‐associated Pathways in Experimental Biliary Atresia

inferredcites →https://doi.org/10.1101/gr.109173.110openalex-snapshot

Tissue-specific disallowance of housekeeping genes: The other face of cell differentiation

inferredcites →https://doi.org/10.1111/j.1399-0004.2010.01436.xopenalex-snapshot

The Human Phenotype Ontology

inferredcites →https://doi.org/10.1111/j.1538-7836.2012.04930.xopenalex-snapshot

Reactome – a curated knowledgebase of biological pathways: megakaryocytes and platelets

inferredcites →https://doi.org/10.1167/iovs.09-4605openalex-snapshot

Gene Expression Profile of Hyperoxic and Hypoxic Retinas in a Mouse Model of Oxygen-Induced Retinopathy

inferredcites →https://doi.org/10.1177/0962280209351908openalex-snapshot

Gene set enrichment analysis made simple

inferredcites →https://doi.org/10.1182/blood-2010-02-270819openalex-snapshot

Identification and functional analysis of endothelial tip cell–enriched genes

inferredcites →https://doi.org/10.1186/1471-2105-11-435openalex-snapshot

CircuitsDB: a database of mixed microRNA/transcription factor feed-forward regulatory circuits in human and mouse

inferredcites →https://doi.org/10.1186/1471-2105-13-s15-s2openalex-snapshot

PAGED: a pathway and gene-set enrichment database to enable molecular phenotype discoveries

inferredcites →https://doi.org/10.1186/1471-2105-6-144openalex-snapshot

PAGE: Parametric Analysis of Gene Set Enrichment

inferredcites →https://doi.org/10.1186/1752-0509-5-87openalex-snapshot

Large-scale analysis of expression signatures reveals hidden links among diverse cellular processes

inferredcites →https://doi.org/10.1186/gb-2004-5-10-r80openalex-snapshot

Bioconductor: open software development for computational biology and bioinformatics

inferredcites →https://doi.org/10.1186/gb-2005-6-9-r81openalex-snapshot

L2L: a simple tool for discovering the hidden significance in microarray expression data

inferredcites →https://doi.org/10.1186/gb-2009-10-8-r84openalex-snapshot

MouseCyc: a curated biochemical pathways database for the laboratory mouse

inferredcites →https://doi.org/10.1186/gb-2010-11-1-r3openalex-snapshot

NetPath: a public resource of curated signal transduction pathways

inferredcites →https://doi.org/10.1261/rna.965408openalex-snapshot

miRDB: A microRNA target prediction and functional annotation database with a wiki interface

inferredcites →https://doi.org/10.1371/journal.pone.0022034openalex-snapshot

Transgenic Overexpression of Tcfap2c/AP-2gamma Results in Liver Failure and Intestinal Dysplasia

inferredcites →https://doi.org/10.1523/jneurosci.0492-05.2005openalex-snapshot

The Genomic Response to Retinal Disease and Injury: Evidence for Endothelin Signaling from Photoreceptors to Glia

inferredcites →https://doi.org/10.1681/asn.2010121308openalex-snapshot

TGF-β/Smad3 Signaling Promotes Renal Fibrosis by Inhibiting miR-29

inferredcites →https://doi.org/10.2147/opth.s3361openalex-snapshot

Hypoxia-ischemia and retinal ganglion cell damage

inferredcites →https://doi.org/10.4137/bbi.s9954openalex-snapshot

The Core Mouse Response to Infection by Neospora Caninum Defined by Gene Set Enrichment Analyses

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Incoming claims: where this work appears in other papers’ reference lists and arguments.

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scTPA: a web tool for single-cell transcriptome analysis of pathway activation signatures

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ShinyGO: a graphical gene-set enrichment tool for animals and plants

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signatureSearch : environment for gene expression signature searching and functional interpretation

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The assisting role of Polη in transcription facilitates formation of damage-induced cohesion

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TET2 deficiency reprograms the germinal center B cell epigenome and silences genes linked to lymphomagenesis

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