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Protocols

Transpath specifications

Information


Unique identifier OMICS_18296
Name Transpath
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Version 8.4
Maintained Yes

Documentation


Maintainers


  • person_outline Satoru Miyano
  • person_outline Masao Nagasaki
  • person_outline Ayumu Saito
  • person_outline Chen Li
  • person_outline Euna Jeong

Publications for Transpath

Transpath citations

 (31)
library_books

Computational master regulator search reveals mTOR and PI3K pathways responsible for low sensitivity of NCI H292 and A427 lung cancer cell lines to cytotoxic action of p53 activator Nutlin 3

2018
BMC Med Genomics
PMCID: 5836833
PMID: 29504919
DOI: 10.1186/s12920-018-0330-5

[…] GSEA) of the obtained three gene expression profiles of differences between sensitive and insensitive lung cancer cell lines. For that we used geneXplain platform and applied the pathways ontology of TRANSPATH® database. The most enriched pathways are presented in the Additional file : Table S3.1 and S3.2 as well as in Fig. .Fig. 5In the Fig.  we selected several TRANSPATH® pathways that demonstra […]

library_books

Pathways of aging: comparative analysis of gene signatures in replicative senescence and stress induced premature senescence

2016
BMC Genomics
PMCID: 5249001
PMID: 28105936
DOI: 10.1186/s12864-016-3352-4

[…] were subjected to functional analysis separately. Each gene was mapped to GO biological processes, GO cellular components, GO molecular functions, Reactome, HumanCyc, TF classification and the latest TRANSPATH® [] available in the geneXplain platform.Caspase-3/keratin-18 and Aurora A kinase/MDM2 pathways were the most upregulated signaling events commonly dominating regulatory landscapes in both b […]

library_books

Computational Identification of Key Regulators in Two Different Colorectal Cancer Cell Lines

2016
Front Genet
PMCID: 4820448
PMID: 27092172
DOI: 10.3389/fgene.2016.00042

[…] Clustering of the most differentially expressed transcriptsAnalysis of differentially expressed transcriptsClustering of the most differentially expressed transcriptsIdentification of overrepresented TRANSPATH pathways based on signature genes (Section 3.3) Pathway analysis for 1638N-T1 (Section 3.3.1)Pathway analysis for CMT-93 (Section 3.3.2)Pathway analysis for 1638N-T1 (Section 3.3.1)Pathway a […]

library_books

Regulatory Divergence of Transcript Isoforms in a Mammalian Model System

2015
PLoS One
PMCID: 4560434
PMID: 26339903
DOI: 10.1371/journal.pone.0137367

[…] r more known SNV or indel between BL6 and CAST (set of 1258 genes used for further analysis).According to Genetrail enrichment analysis, this group was not enriched for any GO term, KEGG, Transfac or Transpath pathway relative to the full set of expressed genes (p < 0.001, not shown), therefore we considered it to be a representative subset. Genes expressing 3, 4 or 5 isoforms were not enriched fo […]

library_books

“Upstream Analysis”: An Integrated Promoter Pathway Analysis Approach to Causal Interpretation of Microarray Data

2015
Microarrays
PMCID: 4996392
PMID: 27600225
DOI: 10.3390/microarrays4020270

[…] A second workflow was designed to find master regulatory molecules in signal transduction pathways upstream of identified transcription factors. The workflow firstly maps transcription factors to the TRANSPATH® network (BIOBASE) [] where they are subjected to a master regulator search with a maximum radius of 10 steps upstream of the factor nodes. A new score is assigned to each potential master r […]

library_books

Hypoxia induces a HIF 1α dependent signaling cascade to make a complex metabolic switch in SGBS adipocytes☆

2014
PMCID: 3969228
PMID: 24275182
DOI: 10.1016/j.mce.2013.11.009

[…] explain software package (BIOBASE). Canonical reaction pathways are a further kind of functional classification, which determines the representation of an input set of molecules to pathways using the transpath tool, which compares the input data to a knowledge base of signal transduction data (). […]

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Transpath institution(s)
Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan

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