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GeneBase specifications

Information


Unique identifier OMICS_19520
Name GeneBase
Restrictions to use None
Community driven No
Data access File download
User data submission Not allowed
Version 1.1
Maintained Yes

Maintainer


  • person_outline Maria Chiara Pelleri

Publication for GeneBase

GeneBase citations

 (5)
library_books

Integrated Quantitative Transcriptome Maps of Human Trisomy 21 Tissues and Cells

2018
Front Genet
PMCID: 5928158
PMID: 29740474
DOI: 10.3389/fgene.2018.00125

[…] ver-/under-expressed genes in that window equal to 1. Since this window size is lower than 40% of the mean size of a human protein-coding gene which was determined to be 67 kb by searching the recent GeneBase database () (mean gene length calculated in 17,958 “reviewed” or “validated” entries available in the NCBI Gene April 2015 annotation release), the significant over-/under-expression of a seg […]

library_books

A molecular view of the normal human thyroid structure and function reconstructed from its reference transcriptome map

2017
BMC Genomics
PMCID: 5604164
PMID: 28923001
DOI: 10.1186/s12864-017-4049-z

[…] d the minimum number of over−/underexpressed genes in that window to 1. This window size is lower than 20% of the 67-kb mean size of a human protein-coding gene (as determined by searching the recent GeneBase database []: mean of gene size from 17,958 “reviewed” or “validated” entries in the NCBI Gene April 2015 annotation release), so the significant over−/underexpression of a segment almost alwa […]

library_books

Transcriptional analysis of abdominal fat in chickens divergently selected on bodyweight at two ages reveals novel mechanisms controlling adiposity: validating visceral adipose tissue as a dynamic endocrine and metabolic organ

2017
BMC Genomics
PMCID: 5559791
PMID: 28814270
DOI: 10.1186/s12864-017-4035-5

[…] on, spot location on slide, and most current gene name/function (based on BLAST score). The gene list were first annotated by clone ID, GenBank ID as determined by BLASTN or BLASTX analysis using the GeneBase function on our laboratory website [].The GPR files were used to determine differential expression in abdominal fat of HG and LG chickens. Log2 transformed median intensity values (for each d […]

library_books

Gamabufotalin triggers c Myc degradation via induction of WWP2 in multiple myeloma cells

2016
Oncotarget
PMCID: 4941272
PMID: 26894970
DOI: 10.18632/oncotarget.7398

[…] Affymetrix Exon array data were processed using the GeneBASE software []. Affymetrix microarray data were processed using the RMA algorithm to compute gene expression levels []. Agilent data were normalized. To determine differentially expressed genes, […]

library_books

Cross hybridization modeling on Affymetrix exon arrays

2008
Bioinformatics
PMCID: 2639301
PMID: 18984598
DOI: 10.1093/bioinformatics/btn571

[…] use these probes were not specifically chosen by Affymetrix to avoid potential cross-hybridization as is the case with the set of background probes (Affymetrix, ). Gene expression was estimated using GeneBASE (Kapur et al., ) on the set of core probes which uniquely map to the transcript, allowing an edit distance of up to 3 bp. […]

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GeneBase institution(s)
Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Bologna, Italy
GeneBase funding source(s)
Supported by ‘RFO’ grants from Alma Mater Studiorum—University of Bologna and Fondazione Umano Progresso, Milano, Italy.

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