GeneMerge protocols

View GeneMerge computational protocol

GeneMerge statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Over-representation analysis chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

GeneMerge specifications

Information


Unique identifier OMICS_18902
Name GeneMerge
Interface Web user interface
Restrictions to use Academic or non-commercial use
Input data A study set gene file; a population set gene file; a gene-association file and a description file.
Output format TXT
Programming languages Perl
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Cristian Castillo-Davis <>

Additional information


Manual: http://www.genemerge.net/GeneMerge1.4-Manual.pdf

Information


Unique identifier OMICS_18902
Name GeneMerge
Software type Application/Script
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input data A study set gene file; a population set gene file; a gene-association file and a description file.
Output format TXT
Operating system Unix/Linux, Mac OS, Windows
Programming languages Perl
Computer skills Advanced
Version 1.4
Stability Stable
Source code URL http://www.genemerge.net/GeneMerge1.4.tar.gz
Maintained Yes

Download


Versioning


Add your version

Documentation


Maintainer


  • person_outline Cristian Castillo-Davis <>

Additional information


Manual: http://www.genemerge.net/GeneMerge1.4-Manual.pdf

Publication for GeneMerge

GeneMerge in pipeline

2010
PMCID: 3055267
PMID: 20663190
DOI: 10.1186/1471-2148-10-227

[…] in the t. dalmanni est database or the homologous regions for d. melanogaster to the frequency of each repeat using a chi-squared goodness of fit test. for the t. dalmanni repeat genes, we then used genemerge with bonferroni adjustment [] to determine if the molecular function represented a nonrandom sample of the putative protein-coding genes in the est database., to assess variation in repeat […]


To access a full list of citations, you will need to upgrade to our premium service.

GeneMerge in publications

 (4)
PMCID: 5873459
PMID: 29562182
DOI: 10.1016/j.celrep.2018.02.085

[…] every protein, we extracted the entire hierarchy of its go terms, i.e., all parents up to the highest level “molecular function” term, and determined the enrichment of go terms in mbs homomers with genemerge (), using all homomers in the pdb as the background set. significances were corrected for multiple testing with the benjamini-hochberg method (a.k.a. false discovery rate [fdr]), […]

PMCID: 3095283
PMID: 20576144
DOI: 10.1186/1471-2229-10-126

[…] at pcc values ≥ 0.7 []. overrepresentation of go slim terms was calculated with hypergeometric distribution followed by a modified bonfferoni correction for multiple testing as implemented in genemerge []. genemerge produced an e-score comparable to a p-value that was used to determine significance of overrepresentation. go slim terms for the entire array were the population set […]

PMCID: 3009504
PMID: 20122205
DOI: 10.1186/1471-2105-11-S1-S32

[…] which are gathered from hprd and kegg. (ii) generate the reference of pathways from 'environmental information processing' and 'cellular processes' categories of kegg pathway maps. (iii) exploiting genemerge method [], produce the pathways set by identifying pathways, which were enriched in the involved genes list of the ppi network from the reference of pathways. (iv) option: incorporate gene […]

PMCID: 2276209
PMID: 18237443
DOI: 10.1186/1471-2164-9-61

[…] band., over- and under-representation of gene ontology (go) terms in the uorf dataset (41 morfs and 7 uorfs with associated go terms) versus the d. melanogaster genome was determined using genemerge v.1.2 [], a program which provides a bonferroni-corrected p-value. association files were derived from gene ontology website files (d. melanogaster annotation received from flybase march […]


To access a full list of publications, you will need to upgrade to our premium service.

GeneMerge institution(s)
Department of Organismic and Evolutionary Biology, Harvard University, Biological Laboratories, Cambridge, MA, USA

GeneMerge reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review GeneMerge