(Q37688372)

22 August 2017

Graphite Web: Web tool for gene set analysis exploiting pathway topology (English)

1 reference

22 August 2017

Gabriele Sales

1

1 reference

22 August 2017

Enrica Calura

series ordinal

2

1 reference

22 August 2017

Paolo Martini

series ordinal

3

1 reference

22 August 2017

Chiara Romualdi

series ordinal

4

1 reference

22 August 2017

language of work or name

English

0 references

publication date

10 May 2013

1 reference

22 August 2017

Nucleic Acids Research

1 reference

22 August 2017

41

1 reference

22 August 2017

Web Server issue

1 reference

22 August 2017

W89-97

1 reference

Creative Commons Attribution-NonCommercial 3.0 Unported

22 August 2017

start time

4 October 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

describes a project that uses

Cytoscape

1 reference

9 June 2022

https://europepmc.org/search?query=(METHODS:'Cytoscape')

based on heuristic

inferred from PubMed Central ID database lookup

limma

1 reference

22 June 2022

https://europepmc.org/article/PMC/3977659

based on heuristic

inferred from PubMed Central ID database lookup

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NetWalker: a contextual network analysis tool for functional genomics

23 August 2017

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SteinerNet: a web server for integrating 'omic' data to discover hidden components of response pathways.

23 August 2017

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graphite - a Bioconductor package to convert pathway topology to gene network.

23 August 2017

1 reference

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EpiRegNet: constructing epigenetic regulatory network from high throughput gene expression data for humans

23 August 2017

1 reference

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Gene set enrichment analysis: performance evaluation and usage guidelines.

23 August 2017

1 reference

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Toll-like receptor genes and their association with colon and rectal cancer development and prognosis

23 August 2017

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ResponseNet: revealing signaling and regulatory networks linking genetic and transcriptomic screening data

23 August 2017

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Hypoxia-induced Jagged2 promotes breast cancer metastasis and self-renewal of cancer stem-like cells

23 August 2017

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Cytoscape 2.8: new features for data integration and network visualization

23 August 2017

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Gene set analysis exploiting the topology of a pathway.

23 August 2017

1 reference

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Cytoscape Web: an interactive web-based network browser

23 August 2017

1 reference

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Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling

23 August 2017

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Gene ontology analysis for RNA-seq: accounting for selection bias

23 August 2017

1 reference

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edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

23 August 2017

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KEGG for representation and analysis of molecular networks involving diseases and drugs

23 August 2017

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Role of Notch signaling in colorectal cancer

23 August 2017

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A general modular framework for gene set enrichment analysis

23 August 2017

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GeneTrailExpress: a web-based pipeline for the statistical evaluation of microarray experiments

23 August 2017

1 reference

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HIF-1alpha and HIF-2alpha have divergent roles in colon cancer.

23 August 2017

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A novel signaling pathway impact analysis.

23 August 2017

1 reference

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Gene-set analysis and reduction

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3977659

Inhibition of JAK1, 2/STAT3 signaling induces apoptosis, cell cycle arrest, and reduces tumor cell invasion in colorectal cancer cells

23 August 2017

1 reference

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Gene-set approach for expression pattern analysis

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3977659

Improving gene set analysis of microarray data by SAM-GS.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3977659

Reactome: a knowledge base of biologic pathways and processes

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3977659

Analyzing gene expression data in terms of gene sets: methodological issues

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3977659

Linear models and empirical bayes methods for assessing differential expression in microarray experiments

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3977659

Calculating the statistical significance of changes in pathway activity from gene expression data

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3977659

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3977659

Discovering statistically significant pathways in expression profiling studies

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3977659

The MAPK signalling pathways and colorectal cancer

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3977659

Comparing functional annotation analyses with Catmap

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3977659

Recognition of commensal microflora by toll-like receptors is required for intestinal homeostasis

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3977659

Colon cancer: genomics and apoptotic events

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3977659

PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3977659

DAVID: Database for Annotation, Visualization, and Integrated Discovery

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3977659

Identifying differentially expressed genes using false discovery rate controlling procedures

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3977659

Does interleukin-6 link explain the link between tumour necrosis, local and systemic inflammatory responses and outcome in patients with colorectal cancer?

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3977659

Onto-Tools: new additions and improvements in 2006.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3977659

Significance analysis of functional categories in gene expression studies: a structured permutation approach

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3977659

A global test for groups of genes: testing association with a clinical outcome

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3977659

Reduced expression of TLR4 is associated with the metastatic status of human colorectal cancer

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3977659

Along signal paths: an empirical gene set approach exploiting pathway topology.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3977659

Gene set enrichment analysis made simple

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3977659

Colon cancer and the immune system: the role of tumor invading T cells

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3977659

Expressions of cell cycle regulators in human colorectal cancer cell lines.

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3977659

23 June 2018

Identifiers

DOI

10.1093/NAR/GKT386

1 reference

22 August 2017

journals/nar/SalesCMR13

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

22 August 2017

1 reference