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Protocols

GSA specifications

Information


Unique identifier OMICS_26980
Name GSA
Alternative name Gene set analysis
Interface Web user interface
Restrictions to use None
Input format TSV,(ZIP+CEL)
Output data A ranked table of differentially expressed meta-genes/pathways and a heat map and box plots for the top-ranked gene sets visualize how the meta- gene expression values differ across different sample groups.
Computer skills Basic
Stability Stable
Maintained Yes

Maintainers


  • person_outline Enrico Glaab
  • person_outline Natalio Krasnogor
  • person_outline Jonathan Garibaldi

Publication for Gene set analysis

GSA citations

 (8)
library_books

Ecological Restoration of Antibiotic Disturbed Gastrointestinal Microbiota in Foregut and Hindgut of Cows

2018
PMCID: 5859144
PMID: 29594071
DOI: 10.3389/fcimb.2018.00079

[…] ndex in both foregut and hindgut demonstrated a high sequencing depth in current analysis (Supplementary Figure ). 16S rRNA gene sequencing reads were deposited in the Genome Sequence Archive (http://gsa.big.ac.cn) in the BIG Data Center under accession numbers PRJCA000455. […]

library_books

Functional Analysis of the FZF1 Genes of Saccharomyces uvarum

2018
Front Microbiol
PMCID: 5808186
PMID: 29467731
DOI: 10.3389/fmicb.2018.00096

[…] y Nextomics Biosciences Co. Ltd using Illumina HiSeq™. The RNA-Seq data were submitted to the Genome Sequence Archive of Beijing Institute of Genomics (BIG) Data Center (publicly accessible at http://gsa.big.ac.cn, Accession No. PRJCA000414). Transcriptome analysis was performed using DEGseq (Wang et al., ) and DESeq (Anders and Huber, ). […]

library_books

Constitutive Expression of miR408 Improves Biomass and Seed Yield in Arabidopsis

2018
Front Plant Sci
PMCID: 5789609
PMID: 29422907
DOI: 10.3389/fpls.2017.02114

[…] ome Sequence Archive () in BIG Data Center (), Beijing Institute of Genomics (BIG), Chinese Academy of Sciences, under accession number CRA000553 that are publicly accessible at http://bigd.big.ac.cn/gsa. […]

call_split

Ribosome Profiling Reveals Genome wide Cellular Translational Regulation upon Heat Stress in Escherichia coli

2017
PMCID: 5673677
PMID: 29031842
DOI: 10.1016/j.gpb.2017.04.005
call_split See protocol

[…] Genome Sequence Archive in BIG Data Center , Beijing Institute of Genomics (BIG), Chinese Academy of Sciences, under accession number CRA 000347, that is publicly accessible at http://bigd.big.ac.cn/gsa. […]

library_books

Drosophila TRF2 and TAF9 regulate lipid droplet size and phospholipid fatty acid composition

2017
PLoS Genet
PMCID: 5362240
PMID: 28273089
DOI: 10.1371/journal.pgen.1006664

[…] 0.001 were considered as differentially expressed for scatter plot representations and for GO term analysis using GOseq []. The raw sequencing data have been submitted to the Genome Sequence Archive (GSA) database with the accession number PRJCA000264. […]

library_books

Down Regulation of EPAS1 Transcription and Genetic Adaptation of Tibetans to High Altitude Hypoxia

2017
Mol Biol Evol
PMCID: 5400376
PMID: 28096303
DOI: 10.1093/molbev/msw280

[…] bases (Q-score ≤ 5) were removed. On an average, we generated 24.5 million paired-end reads for each sample. The RNAseq data was deposited in an open-access archive (Genome Sequence Achieve at http://gsa.big.ac.cn) and the accession numbers are PRJCA000268 and PRJCA000269.Pre-processed RNA-Seq reads were mapped to the genome using split-mapping aligner STAR (release 2.4.1a) (), and the resulting b […]

Citations

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GSA institution(s)
School of Computer Science, Nottingham University, Nottingham, UK
GSA funding source(s)
Supported by the Marie-Curie Early-Stage-Training programme (grant MEST-CT-2004-007597), by the UK Engineering and Physical Sciences Research Council (EP/E017215/1) and the Biotechnology and Biological Sciences Research Council (BB/F01855X/1).

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