SubpathwayMiner statistics

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Citations per year

Number of citations per year for the bioinformatics software tool SubpathwayMiner
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Tool usage distribution map

This map represents all the scientific publications referring to SubpathwayMiner per scientific context
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SubpathwayMiner specifications

Information


Unique identifier OMICS_12661
Name SubpathwayMiner
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data SubpathwayMiner supports three types of inputting data: gene list, compound list, gene and compound list.
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Version 3.1
Stability No
Source code URL https://cran.r-project.org/src/contrib/Archive/SubpathwayMiner/
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Xia Li

Information


Unique identifier OMICS_12661
Name SubpathwayMiner
Interface Web user interface
Restrictions to use None
Input data SubpathwayMiner supports three types of inputting data: gene list, compound list, gene and compound list.
Programming languages R
Computer skills Basic
Stability No
Maintained Yes

Documentation


Maintainer


  • person_outline Xia Li

Publication for SubpathwayMiner

SubpathwayMiner citations

 (6)
library_books

Characterization of dysregulated lncRNA mRNA network based on ceRNA hypothesis to reveal the occurrence and recurrence of myocardial infarction

2018
PMCID: 5841419
PMID: 29531832
DOI: 10.1038/s41420-018-0036-7

[…] perated mice in a recently published study.We further examined the biological function of the DLMN_MI_OC and DLMN_MI_Re. Significantly enriched KEGG biological subpathways were identified by applying SubpathwayMiner using 235 mRNAs in the DLMN_MI_OC and 95 mRNAs in the DLMN_MI_Re. Consequently, 36 and 43 significant subpathways were obtained with a p-value of <0.05 (Supplementary Table ). To more […]

library_books

Adropin deficiency worsens HFD induced metabolic defects

2017
PMCID: 5596552
PMID: 28837146
DOI: 10.1038/cddis.2017.362

[…] responsive element binding protein 3-like 3 (Creb3l3), 5-hydroxytryptamine (serotonin) receptor 1D (Htr1d), and UDP-Gal: beta-GlcNAc beta 1,3-galactosyltransferase, polypeptide 5 (B3galt5). GOSim and SubpathwayMiner were employed for enrichment analysis of coding genes from each specific cluster based on GO terms and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways. Each cluster was annotat […]

library_books

CALCB splice region pathogenic variants leading to plasma cell neurotropic enrichment in type 1 autoimmune pancreatitis

2017
PMCID: 5386480
PMID: 28151472
DOI: 10.1038/cddis.2017.32

[…] em Disorders' (P=9.67E-06, Activation z-score=2.526). The down-regulated genes are mainly enriched in the function of glycosphingolipid biosynthesis (P=9.26E-10, Activation z-score=−2.143). GOSim and SubpathwayMiner were employed for enrichment analyses of coding genes from each specific clusters based on GO terms and KEGG pathways, and each cluster was annotated with the enriched functions of the […]

library_books

Integrating subpathway analysis to identify candidate agents for hepatocellular carcinoma

2016
PMCID: 4788366
PMID: 27022281
DOI: 10.2147/OTT.S97211

[…] acy for HCC by integrating the association between small molecules and subpathways. A study by Li et al also identified global associations between 403 metabolic subpathways and 488 known drugs using SubpathwayMiner with k=3. However, in that study, only metabolic subpathways were investigated rather than all kinds of pathways. Some signaling pathways also play an important role in drug response. […]

library_books

Identification of novel genes and pathways in carotid atheroma using integrated bioinformatic methods

2016
Sci Rep
PMCID: 4705461
PMID: 26742467
DOI: 10.1038/srep18764

[…] on software packages were identified using the hypergeometric tests with an adjusted p-value <0.01, calculated by the Benjamini-Hochberg method. Pathway-enrichment analysis was done using the R-based SubpathwayMiner software packages. Significantly enriched pathways were identified using hypergeometric tests and a p-value <0.01 was applied as the cut-off value for statistical significance.Validati […]

library_books

Dissection of miRNA miRNA Interaction in Esophageal Squamous Cell Carcinoma

2013
PLoS One
PMCID: 3764179
PMID: 24039884
DOI: 10.1371/journal.pone.0073191

[…] genes and subpathway are shown in .In total, we obtained 35942 miRNA-target regulations for these 56 miRNAs. miRNA-subpathway networks were constructed based on target gene enrichment analysis by the SubpathwayMiner package. In the miRNA-subpathway network, a miRNA and a subpathway were connected if the target genes of this miRNA were significantly enriched in this subpathway (P<0.05). To ensure t […]


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SubpathwayMiner institution(s)
College of Bioinformatics Science and Technology and Bio-pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin, China; Princess Margaret Hospital in University Health Network, Toronto, ON, Canada
SubpathwayMiner funding source(s)
The National Natural Science Foundation of China (grant nos. 30871394, 30370798 and 30571034), the National High Tech Development Project of China, the 863 Program (grant nos. 2007AA02Z329), the National Basic Research Program of China, the 973 Program (grant nos. 2008CB517302) and the National Science Foundation of Heilongjiang Province (grant nos. ZJG0501, 1055HG009, GB03C602-4, and BMFH060044)

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