GeneCodis protocols

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GeneCodis specifications

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Unique identifier OMICS_02221
Name GeneCodis
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained No

Publication for GeneCodis

GeneCodis in pipelines

 (32)
2017
PMCID: 5227060
PMID: 27908864
DOI: 10.1302/2046-3758.512.BJR-2016-0073.R1

[…] analysis were performed to detect the biological functions and potential pathway of degs. go-rilla, a web-accessible programme was used for go enrichment analysis. the online-based software genecodis was used in pathway enrichment analysis based on the kegg pathway database which is a recognised and comprehensive database including an extensive array of biochemistry pathways., the ppis […]

2017
PMCID: 5237304
PMID: 28086821
DOI: 10.1186/s13000-016-0596-x

[…] expressed genes (degs). heat map analysis was conducted using the “heatmap.2” function of the r/bioconductor package “gplots” []., the go and pathway enrichment was analyzed via the online software genecodis to facilitate the interpretation of biological roles of degs (http://genecodis.cnb.csic.es) []. the go functions of the degs were determined according to different categories including […]

2017
PMCID: 5316826
PMID: 28193997
DOI: 10.1038/ncomms14127

[…] located above (red) or below (blue) the mean, respectively). adjusted p values were corrected for multiple testing using the benjamini–hochberg method. gene ontology analysis was performed using the genecodis application., c57bl/6-ins2akita/j (ref. ), tgif1tm1apah (ref. ) and tg(sox2-cre)1amc/j (ref. ) (jax laboratories) mouse strains were previously described. the mouse tgif2tm1a(eucomm)wtsi […]

2017
PMCID: 5356255
PMID: 28302135
DOI: 10.1186/s12974-017-0834-5

[…] set of genes linked by outer literature databases (metacore™; additional file : figure s1d) and within the distance measures of experiment data (additional file : figure s1e)., finally, we used the genecodis platform [] to obtain deg enrichment in different annotation databases, specifically for gene ontology (go) terms for biological process (fig. ), and for the kyoto encyclopedia of genes […]

2017
PMCID: 5356478
PMID: 28316886
DOI: 10.7717/peerj.3078

[…] were filtered as degs. in order to understand the biological roles of degs, the kyoto encyclopedia of genes and genomes (kegg) pathway and gene ontology (go) terms were enriched by the online tool genecodis3 (; ; ). the threshold of go function and kegg pathway enrichment were fdr < 0.05., in order to explore the interaction between the top 10 up- and down-regulated degs in synovial tissues […]

GeneCodis in publications

 (252)
PMCID: 5955888
PMID: 29769614
DOI: 10.1038/s41598-018-25717-w

[…] of cells expressing either p110α with akt1 or kinase-dead akt1k179m were compared. table  show the 81 genes that were up-regulated over 1.7-fold and 39 genes down-regulated below 0.6-fold. genecodis and go term finder analyses on up-regulated genes highlighted three significantly enriched functional categories: “pentose phosphate shunt” (p-value = 9×10−15 by chi square test […]

PMCID: 5935809
PMID: 29203636
DOI: 10.1302/2046-3758.612.BJR-2017-0102.R1

[…] false discovery rates (fdr) were further calculated. fdr < 0.01 was selected as the threshold for screening degs., go and kegg enrichment analyses were carried out for the identified degs using genecodis3 (http://www.genecodis.cnb.csic.es/analysis).- significant go terms and kegg pathways were identified according to the threshold of p < 0.05., to gain deeper insight into the molecular […]

PMCID: 5909781
PMID: 29713155
DOI: 10.2147/COPD.S163459

[…] pictar, mirdb and targetscan. validated targets were acquired from tarbase. briefly, we took the intersection of the three series of predicted targets and validated the targets using tarbase., genecodis is a web-based tool for comprehensive analysis of gene annotations, encompassing go, panther and kyoto encyclopedia of genes and genomes (kegg) pathways, interpro motifs and transcription […]

PMCID: 5875763
PMID: 29596435
DOI: 10.1371/journal.pone.0193427

[…] to further understand the biological function of tumor differentiation related genes in pancreatic adenocarcinoma, we performed the go functional categories and the kegg biochemical pathway using genecodis3 (http://genecodis.cnb.csic.es/analysis). false discovery rate < 0.05 was considered to be statistically significant., in order to assess the diagnostic value of tumor differentiation […]

PMCID: 5881766
PMID: 29568943
DOI: 10.3892/ijmm.2018.3575

[…] annotation, including gene ontology (go) function and kyoto encyclopedia of genes and genomes (kegg) pathway enrichment analyses of the demrnas co-expressed with delncrnas was performed using the genecodis3 tool (http://genecodis.cnb.csic.es/analysis). a hypergeometric test was used to obtain the p-value. the false discovery rate (fdr; corrected p-value) of <0.05 was set as the cut-off […]

GeneCodis institution(s)
Functional Bioinformatics Group, National Center for Biotechnology (CNB-CSIC), Madrid, Spain

GeneCodis review

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k.4ughi

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Web
a good website for GO and KEGG pathway analysis