(Q42095799)

16 October 2017

Deriving transcriptional programs and functional processes from gene expression databases (English)

1 reference

16 October 2017

Jeffrey T Chang

1

1 reference

PMC publication ID

3324522

16 October 2017

language of work or name

English

0 references

publication date

8 March 2012

1 reference

16 October 2017

8

1 reference

inferred from page(s)

published in

Bioinformatics

1 reference

16 October 2017

28

1 reference

16 October 2017

8

1 reference

16 October 2017

1122-1129

1 reference

Molecular signatures database (MSigDB) 3.0.

16 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3324522

Content-based microarray search using differential expression profiles

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3324522

NCBI GEO: archive for functional genomics data sets--10 years on

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3324522

Genome profiling of ERBB2-amplified breast cancers

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3324522

Independent component analysis: mining microarray data for fundamental human gene expression modules

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3324522

A pathway-based classification of human breast cancer.

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3324522

An atlas of combinatorial transcriptional regulation in mouse and man

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3324522

Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3324522

GEOGLE: context mining tool for the correlation between gene expression and the phenotypic distinction

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3324522

Latent bone metastasis in breast cancer tied to Src-dependent survival signals

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3324522

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3324522

Singular value decomposition-based regression identifies activation of endogenous signaling pathways in vivo

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3324522

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

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3324522

GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3324522

Nuclear architecture and gene regulation

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3324522

Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3324522

Genome-wide transcriptional analysis of the human cell cycle identifies genes differentially regulated in normal and cancer cells

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3324522

An E2F1-dependent gene expression program that determines the balance between proliferation and cell death

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3324522

JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3324522

TREMOR--a tool for retrieving transcriptional modules by incorporating motif covariance.

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3324522

Systematic discovery of functional modules and context-specific functional annotation of human genome

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3324522

Genome-wide mapping of in vivo protein-DNA interactions

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3324522

Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3324522

Clustering by passing messages between data points

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3324522

The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3324522

TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3324522

Oncogenic pathway signatures in human cancers as a guide to targeted therapies

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3324522

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

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3324522

An expression signature for p53 status in human breast cancer predicts mutation status, transcriptional effects, and patient survival

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3324522

The E2F transcriptional network: old acquaintances with new faces

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3324522

E2Fs link the control of G1/S and G2/M transcription

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3324522

Transcriptional regulatory code of a eukaryotic genome

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3324522

Outcome signature genes in breast cancer: is there a unique set?

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3324522

CleanEx: a database of heterogeneous gene expression data based on a consistent gene nomenclature

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3324522

Identifying cooperativity among transcription factors controlling the cell cycle in yeast

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3324522

Identification of E-box factor TFE3 as a functional partner for the E2F3 transcription factor

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3324522

Prediction and uncertainty in the analysis of gene expression profiles.

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3324522

Interaction of YY1 with E2Fs, mediated by RYBP, provides a mechanism for specificity of E2F function

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3324522

Identification of genes periodically expressed in the human cell cycle and their expression in tumors

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3324522

Sibling rivalry in the E2F family

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3324522

Identifying regulatory networks by combinatorial analysis of promoter elements

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3324522

Role for E2F in control of both DNA replication and mitotic functions as revealed from DNA microarray analysis

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3324522

Molecular portraits of human breast tumours

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3324522

Functional discovery via a compendium of expression profiles

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3324522

Gene ontology: tool for the unification of biology

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3324522

Systematic determination of genetic network architecture

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3324522

Interaction of Sp1 with the growth- and cell cycle-regulated transcription factor E2F

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3324522

E2F1 overexpression in quiescent fibroblasts leads to induction of cellular DNA synthesis and apoptosis.

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3324522

Regulation of a Segmentation Stripe by Overlapping Activators and Repressors in the Drosophila Embryo

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3324522

Exploring the functional landscape of gene expression: directed search of large microarray compendia

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3324522

GATHER: a systems approach to interpreting genomic signatures

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3324522

Predicting gene expression from sequence

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3324522

GEST: a gene expression search tool based on a novel Bayesian similarity metric.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3324522

Gene expression informatics--it's all in your mine.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3324522

Toward an understanding of the functional complexity of the E2F and retinoblastoma families

17 August 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22408194

12 December 2020

inferred from PubMed ID database lookup

Identifiers

DOI

10.1093/BIOINFORMATICS/BTS112

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/wja3ovsnnrfnrg3a5me3qd6j44

30 July 2022

journals/bioinformatics/Chang12

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

release_wja3ovsnnrfnrg3a5me3qd6j44

28 January 2021

Fatcat ID

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/wja3ovsnnrfnrg3a5me3qd6j44

30 July 2022

https://api.fatcat.wiki/v0/release/wja3ovsnnrfnrg3a5me3qd6j44

1 reference

30 July 2022

https://api.fatcat.wiki/v0/release/wja3ovsnnrfnrg3a5me3qd6j44

PubMed publication ID

1 reference

30 July 2022