GOSSIP protocols

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GOSSIP specifications

Information


Unique identifier OMICS_19193
Name GOSSIP
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Windows
Computer skills Advanced
Stability Stable
Registration required Yes

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Publication for GOSSIP

GOSSIP in pipelines

 (7)
2017
PMCID: 5408325
PMID: 28503180
DOI: 10.3389/fpls.2017.00634

[…] ka/ks > 0.5, and a reference dataset with ka/ks value < 0.5. the significance of the difference in go term abundance between the two datasets was tested using the fisher's exact test with the gossip package (blüthgen et al., ) implemented in blast2go v.2.6.0 (conesa et al., )., total rna was extracted as described above. polyadenylated rna was isolated and translated into cdna using oligo […]

2016
PMCID: 4782317
PMID: 26956617
DOI: 10.1186/s12864-016-2546-0

[…] blast2go suite []. functional characterization and gene ontology (go) categories for cellular functions, cellular components, and biological processes, were assigned using the blast2go platform. the gossip function was utilized to determine go term enrichment in different comparisons []. manual annotation of specific genes was performed by using blast searches against the ncbi databases (e value  […]

2016
PMCID: 4855978
PMID: 27142227
DOI: 10.1186/s12864-016-2639-9

[…] in one of the analyzed condition and with at least six counts among all conditions. in this analysis, blast2go [] was used to compute enriched go terms applying fisher’s exact test as implemented in gossip [, ]. go terms with 0.05 fdr and q-value ≤ 0.05 were considered as significantly enriched in each comparison., rna-seq were deposited in the ncbi biosample database […]

2015
PMCID: 4362301
PMID: 25852698
DOI: 10.3389/fpls.2015.00122

[…] method. the gene ontology (go) terms were loaded in the blast2go suite v.2.7.2 (conesa et al., ; conesa and götz, ) in order to statistically analyze go-term enrichment. blast2go integrated the gossip package for statistical assessment of differences in go-term abundance between two sets of sequences (blüthgen et al., ). this package uses fisher's exact test and corrects for multiple […]

2012
PMCID: 3421235
PMID: 22904672
DOI: 10.7150/ijbs.4469

[…] rna-binding, seg and superfamily) on the predicted orfs., the analysis of the enrichment in go-term between male and female transcriptomes was performed with the blast2go application using gossip . go-terms in female data (female singletons + contigs assembled from female ests only) (test group) were tested for enrichment compared to male data (male singletons + contigs assembled […]


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GOSSIP in publications

 (40)
PMCID: 5654045
PMID: 29061117
DOI: 10.1186/s12864-017-4210-8

[…] through blastx search against kegg database and cog database, respectively [, ]. the difference in go term abundance between the two species was analysed using fisher’s exact test with the gossip package [] implemented in blast2go, with support from p-value and subsequently the false detection rate (fdr) at 0.05., meiosis was induced in cultures by reduction of the nutrient levels […]

PMCID: 5462986
PMID: 28642749
DOI: 10.3389/fmicb.2017.01036

[…] relative enrichment (overrepresentation) of go terms for up-regulated genes compared to a background of go terms for all genes was assessed using fisher exact tests. the test was performed using the gossip statistical package () implemented within blast2go. the false discovery rate (fdr) procedure of was used to correct for multiple hypothesis testing (fdr = 0.05)., to gain further insights […]

PMCID: 5408325
PMID: 28503180
DOI: 10.3389/fpls.2017.00634

[…] ka/ks > 0.5, and a reference dataset with ka/ks value < 0.5. the significance of the difference in go term abundance between the two datasets was tested using the fisher's exact test with the gossip package (blüthgen et al., ) implemented in blast2go v.2.6.0 (conesa et al., )., total rna was extracted as described above. polyadenylated rna was isolated and translated into cdna using oligo […]

PMCID: 5026262
PMID: 27499133
DOI: 10.1093/molbev/msw161

[…] rest of the genome, of go terms in the subsets of genes included in the deletions, interrupted by insertions or showing differential coverage was tested using a fisher’s exact test implemented in the gossip package () integrated in blast2go. to reduce the number of false positives, a false discovery rate correction for multiple testing () was applied and only differences with a corrected p-value & […]

PMCID: 4782317
PMID: 26956617
DOI: 10.1186/s12864-016-2546-0

[…] blast2go suite []. functional characterization and gene ontology (go) categories for cellular functions, cellular components, and biological processes, were assigned using the blast2go platform. the gossip function was utilized to determine go term enrichment in different comparisons []. manual annotation of specific genes was performed by using blast searches against the ncbi databases (e value  […]


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GOSSIP institution(s)
Institute for Theoretical Biology, Humboldt University Berlin, Germany; Pathologisches Institut, Ruprecht-Karls-Universitat Heidelberg, Germany; MicroDiscovery GmbH , Berlin, Germany
GOSSIP funding source(s)
Supported by the Deutsche Forschungsgemeinschaft (SFB 618) and the BMBF grant number 01GR0444.

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