GeneProf protocols

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GeneProf specifications

Information


Unique identifier OMICS_00442
Name GeneProf
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability No
Maintained No

Maintainer


This tool is not available anymore.

Publication for GeneProf

GeneProf in pipeline

2016
PMCID: 5003112
PMID: 27428510
DOI: 10.1038/nchembio.2132

[…] analysis of the ngs data was performed as previously described. in brief, sequences were uploaded to the web-based sequence-analysis platform geneprof. at first, the reads were filtered according to quality using the modify and filter sequence tool (modify: cut after low quality 10; filter: cumulative quality score > 300; discard […]


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GeneProf in publications

 (26)
PMCID: 5802454
PMID: 29317601
DOI: 10.1038/s41398-017-0057-7

[…] console was used for determination of significant differential expression in microarray experiments, with an fdr p-value of 0.75 (benjamini−hochberg). enrichment analysis was conducted using the geneprof hypergeometric probability calculator (https://www.geneprof.org/geneprof/tools/hypergeometric.jsp)., lineage tracing was conducted as previously described. male gli1tm3(cre/ert2)alj/j mice […]

PMCID: 5716029
PMID: 29093060
DOI: 10.1084/jem.20162012

[…] library preparation and cdna sequencing was performed in the edinburgh genomics facility at the university of edinburgh., sequencing reads were processed using the rna-seq analysis pipelines of geneprof (). in brief, sequencing reads were aligned to mouse genome ncbi37/mm9 with tophat (trapnell et al., 2009) v1.2.0 (2012-11-14) and bowtie () v0.12.3 (2012-04-10). the mrna levels per gene […]

PMCID: 5656305
PMID: 29069077
DOI: 10.1371/journal.pgen.1006864

[…] leaving 11103 genes. overlap between datasets was determined and visualized as a venn diagram by biovenn [] (figs and ). hypergeometric statistics on overlaps were calculated using https://www.geneprof.org/geneprof/tools/hypergeometric.jsp., the raw data for rna-seq and chip-seq is available at the ncbi gene expression omnibus (geo), accession number gse89459., diagnostic whole exome […]

PMCID: 5447181
PMID: 28611744
DOI: 10.3389/fmicb.2017.00940

[…] of orthologous groups (cog) (galperin et al., ) as previously described in ia3902 (wu et al., ) with statistical significance calculated using hypergeometric probability testing (https://www.geneprof.org/) (halbritter et al., ). venn diagrams depicting overlap of genes differentially regulated in multiple conditions were generated using the venny website […]

PMCID: 5737374
PMID: 28338930
DOI: 10.1093/dnares/dsx009

[…] biologist with only wet lab experience. s-mart focuses on the detection of alternative splicing and transcript isoforms, and differentially expressed genes also can be identified. although funrich, geneprof and microscope can conduct go enrichment analysis, differential expression analysis and network construction, visual pathway and co-expression analysis are unavailable in these systems. […]


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GeneProf institution(s)
Institute for Stem Cell Research, Centre for Regenerative Medicine, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
GeneProf funding source(s)
Supported by a Medical Research Council studentship and by the European Commission Seventh Framework Programme ‘EuroSyStem’.

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