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GEDA specifications

Information


Unique identifier OMICS_15790
Name GEDA
Alternative name Gene Expression Data Analyzer
Interface Web user interface
Restrictions to use None
Output data The GEDA tool output includes frequency histogram for two groups and, if requested, individual histograms.
Computer skills Basic
Stability No
Maintained No

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This tool is not available anymore.

Publication for Gene Expression Data Analyzer

GEDA citations

 (8)
library_books

Transformation of metabolism with age and lifestyle in Antarctic seals: a case study of systems biology approach to cross species microarray experiment

2010
BMC Syst Biol
PMCID: 2958164
PMID: 20920245
DOI: 10.1186/1752-0509-4-133

[…] A set of differentially expressed genes was selected using the University of Pittsburgh Gene Expression Data Analysis suite (GEDA, http://bioinformatics.upmc.edu/GE2/GEDA.html). For selection, we applied the standard J5 metric with threshold 4 and optional 4 iterations of the Jackknife procedure to reduce the number of fals […]

library_books

Computational analysis of gene expression space associated with metastatic cancer

2009
BMC Bioinformatics
PMCID: 3226195
PMID: 19811690
DOI: 10.1186/1471-2105-10-S11-S6

[…] A set of differentially expressed genes was selected using University of Pittsburgh Gene Expression Data Analysis suite (GEDA)[]. The software is available for downloading from http://bioinformatics.upmc.edu/GE2/GEDA.html. For selection, we applied the standard J5 metric with threshold 4 and optional 4 iteration of Jack […]

call_split

Transcriptional Profiling of Bacillus anthracis Sterne (34F2) during Iron Starvation

2009
PLoS One
PMCID: 2742718
PMID: 19768119
DOI: 10.1371/journal.pone.0006988
call_split See protocol

[…] Analysis of the microarray data was carried out using Gene Expression Data Analyzer (GEDA; http://bioinformatics.upmc.edu/GE2/GEDA.html) . Briefly, this online software package was used for statistical comparisons of individual conditions at each timepoi […]

call_split

Global transcriptional response to mammalian temperature provides new insight into Francisella tularensis pathogenesis

2008
BMC Microbiol
PMCID: 2576331
PMID: 18842136
DOI: 10.1186/1471-2180-8-172
call_split See protocol

[…] ed with Agilent wash buffers before being scanned on an Agilent microarray scanner. At least 3 separate RNA extractions were used for each condition tested by microarray (26°C or 37°C-grown bacteria).Gene Expression Data Analyzer (GEDA; ) was utilized for analysis of the microarray data []. This online software package was used for minimum mean ratio array normalization followed by log2 transforma […]

library_books

Systems biology approach to identification of biomarkers for metastatic progression in cancer

2008
BMC Bioinformatics
PMCID: 2537559
PMID: 18793472
DOI: 10.1186/1471-2105-9-S9-S8

[…] A set of differentially expressed genes was selected using University of Pittsburgh Gene Expression Data Analysis suite (GEDA, ). For selection, we applied the standard J5 metric with threshold 4 and optional 4 iteration of Jackknife procedure to reduce the number of false-positive differential genes []. Both J5 metric […]

library_books

In praise of arrays

2008
PMCID: 2719727
PMID: 18568367
DOI: 10.1007/s00467-008-0808-z

[…] is of microarrays (PAM; http://www-stat.stanford.edu/tibs/PAM/),Expression Profiler: next generation (EP:NG; http://www.ebi.ac.uk/expressionprofiler),Bioconductor (http://www.bioconductor.org),Cancer gene expression data analyzer (caGEDA; http://bioinformatics.upmc.edu/GE2/GEDA.html),Analysis of microarray data (AMIADA; http://dambe.bio.uottawa.ca/amiada.asp),GenePattern (http://www.broad.mit.edu/ […]

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GEDA institution(s)
Center for Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, USA

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