SubpathwayMiner protocols

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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

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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 in pipelines

 (3)
2016
PMCID: 4705461
PMID: 26742467
DOI: 10.1038/srep18764

[…] extracts biologically relevant terms from statistically significant go terms for a disease., the degs were chosen for further analysis of kyoto encyclopedia of gene and genome (kegg) enrichment. the subpathwayminer is a pathway identification system and accurately assessed the pathway structure to locate disease-relevant kegg pathways and subpathways in degs relative to the genomic background., […]

2012
PMCID: 3508620
PMID: 22472218
DOI: 10.1186/2043-9113-2-8

[…] coordinates. ontologizer 2.0, a go term enrichment tool with command-line interface and improved statistical method for deriving go terms enriched in a given list of proteins was used in this study. subpathwayminer, an r package that internally handles kegg annotations for pathway enrichment analysis were used to derive statistically significant pathways associated with the dataset. enriched […]

2012
PMCID: 3508620
PMID: 22472218
DOI: 10.1186/2043-9113-2-8

[…] summary of the bioinformatics pipeline employed in this study is depicted in figure ., protein domain enrichment analysis was performed using david []. kegg pathway analysis was performed using subpathwayminer [] and disease ontology analysis was performed using functional disease ontology server [,]., to perform protein domain enrichment analysis, domains were identified in proteins […]


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SubpathwayMiner in publications

 (24)
PMCID: 5902927
PMID: 29661250
DOI: 10.1186/s13058-018-0953-7

[…] > 2) were selected from microarray data, and the candidate genes were mapped onto the kyoto encyclopedia of genes and genomes pathways based on the enzyme commission numbers by using the r package subpathwayminer v.3.1. subsequently, the hypergeometric test was performed to identify significantly enriched pathways and calculate the false-positive discovery rate in terms of the p value., α-kg wa […]

PMCID: 5845323
PMID: 29523145
DOI: 10.1186/s12943-018-0821-1

[…] and ≤ 0.5) were selected from microarray data and candidate genes were mapped onto the kyoto encyclopedia of genes and genomes pathways based on the enzyme commission numbers by using the r package subpathwayminer v.3.1. subsequently, a hypergeometric test was performed to identify significantly enriched pathways and calculate the false-positive discovery rate in the false discovery […]

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

[…] 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 ). […]

PMCID: 5783834
PMID: 29154475
DOI: 10.1111/jcmm.13376

[…] pathways were obtained from the kegg pathway database. three hundred and forty‐three kegg pathways were obtained, including 152 metabolic and 191 non‐metabolic pathways. we used the r package subpathwayminer to reconstruct all pathways graphically . this type of reconstruction retained the raw information of the pathways, particularly the structures, and provided detailed and reliable […]

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

[…] 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 […]


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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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