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Protocols

GeneAnnot specifications

Information


Unique identifier OMICS_22465
Name GeneAnnot
Restrictions to use None
Database management system MySQL
Community driven No
Data access Browse
User data submission Not allowed
Maintained Yes

Maintainers


  • person_outline Alessandro Coppe
  • person_outline Stefania Bortoluzzi
  • person_outline Francesco Ferrari
  • person_outline Alexandra Sirota
  • person_outline Marilyn Safran

Publications for GeneAnnot

GeneAnnot citations

 (17)
library_books

TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages

2016
F1000Res
PMCID: 5302158
PMID: 28232861
DOI: 10.5256/f1000research.9601.r14695

[…] or samples), but the user can relabel the samples to compare different groups. For the next sections, we will work with both the experimental group (LGG) and control group (GBM). 1 library (ELMER) 2 geneAnnot <– txs() 3 geneAnnot $ GENEID <– paste0( "ID" ,geneAnnot $ GENEID) 4 geneInfo <– promoters(geneAnnot,upstream = 0, downstream = 0) 5 probe <– get .feature.probe() 6 7 # create mee object, us […]

call_split

Regulation of IL 20 Expression by Estradiol through KMT2B Mediated Epigenetic Modification

2016
PLoS One
PMCID: 5091760
PMID: 27806114
DOI: 10.1371/journal.pone.0166090
call_split See protocol

[…] The microarray raw data deposited in ArrayExpress (accession E-MTAB-4923) was preprocessed with the justRMA function of the affy Bioconductor package [] with GeneAnnot based custom CDF (gahgu133plus2 v2.2.1) []. The log-2 normalized intensities were adjusted for batch effects by using ComBat function of the sva Bioconductor package []. The cmdscale functio […]

library_books

Transcriptional, epigenetic and retroviral signatures identify regulatory regions involved in hematopoietic lineage commitment

2016
Sci Rep
PMCID: 4837375
PMID: 27095295
DOI: 10.1038/srep24724

[…] orescence signals to log2 expression values, we used the robust multi-array average procedure RMA of the Bioconductor affy package and the HG-U133 Plus 2.0 custom Chip Definition Files (CDF) based on GeneAnnot. We used Principal Component Analysis (PCA) coded by the prcomp function of the R stats package to verify the reproducibility of the 3 biological replicates. We used DNA-Chip Analyzer (dChip […]

library_books

Improving Cancer Gene Expression Data Quality through a TCGA Data Driven Evaluation of Identifier Filtering

2015
Cancer Inform
PMCID: 4686346
PMID: 26715829
DOI: 10.4137/CIN.S33076

[…] to a different chromosome, strand, or are part of a gene cluster that could cause cross-hybridization. The CDF file can be obtained from http://masker.nci.nih.gov/ev/.We test three filters utilizing Geneannot, a database of gene expression annotations and quality that evaluates the Affymetrix probesets on the following criteria. For each of the probesets on the Affymetrix chip, sensitivity, speci […]

library_books

Genome Wide Definition of Promoter and Enhancer Usage during Neural Induction of Human Embryonic Stem Cells

2015
PLoS One
PMCID: 4433211
PMID: 25978676
DOI: 10.1371/journal.pone.0126590

[…] ording to the manufacturer protocol (Affymetrix, Santa Clara, CA). Signals were converted to expression values by the RMA algorithm [] and HG-U133 Plus 2.0 custom Chip Definition Files (CDF) based on GeneAnnot []. Differentially expressed genes were identified by Significance Analysis of Microarray method (SAM, []) setting the q-value [] threshold equal to 0 (or ≤0.01) and considering fold change […]

library_books

RUNX1/ETO blocks selectin mediated adhesion via epigenetic silencing of PSGL 1

2015
Oncogenesis
PMCID: 5399174
PMID: 25867177
DOI: 10.1038/oncsis.2015.6

[…] A). Hybridization and image acquisition followed official Affymetrix protocols. No cell sorting was performed. For probes to probe set annotation, we used custom chip definition files (CDFs) based on GeneAnnot version 2.0, synchronized with GeneCards Version 3.04 (available at http://www.xlab.unimo.it/GA_CDF/). These CDFs decrease the total number of probe sets (one probe set per gene), and potent […]

Citations

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GeneAnnot institution(s)
Department of Biomedical Sciences, University of Modena and Reggio Emilia, Modena, Italy; Department of Biology, University of Padova, Padova, Italy; Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, Israel; Department of Biological Services, The Weizmann Institute of Science, Rehovot, Israel; Bioinformatics Knowledge Unit, The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering Technion, Israel Institute of Technology, Haifa, Israel; Department of Chemical Engineering Processes, University of Padova, Padova, Italy
GeneAnnot funding source(s)
Supported by grants from the Italian Ministry of University and Research (PRIN2005050779 and PRIN2005069853), OncoSuisse Collaborative Cancer Research (OCS-1939-8-2006), the University of Padova (CPDA065788/06, CPDR064110 and CPDR074285), Fondazione Cassa di Risparmio di Padova e Rovigo (Progetti di Eccellenza 2006), the Weizmann Institute of Science Crown Human Genome Center and the Abraham and Judith Goldwasser Fund.

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