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RefGene specifications

Information


Unique identifier OMICS_17100
Name RefGene
Restrictions to use None
Community driven No
Data access Browse
User data submission Not allowed
Maintained No

Taxon


  • Primates
    • Homo sapiens

Maintainer


This tool is not available anymore.

RefGene citations

 (216)
call_split

Dependence receptor UNC5A restricts luminal to basal breast cancer plasticity and metastasis

2018
PMCID: 5932758
PMID: 29720215
DOI: 10.1186/s13058-018-0963-5
call_split See protocol

[…] 9700).We used STAR RNA-Seq aligner to map all sequence libraries to the human genome (UCSC hg19) [] followed by the assignment of uniquely mapped reads to individual genes based on annotation of hg19 refGene by featureCounts []. After trimmed mean of M values (TMM) normalization, gene expression profiling was summarized on the base-2 logarithmic scale. Genes with an average expression level lower […]

call_split

Characterization of Wnt and Notch Responsive Lgr5+ Hair Cell Progenitors in the Striolar Region of the Neonatal Mouse Utricle

2018
PMCID: 5937014
PMID: 29760650
DOI: 10.3389/fnmol.2018.00137
call_split See protocol

[…] e expression of every gene was measured by FPKM (Fragments Per Kilobase of transcript per Million fragments mapped). Genes and transcripts were annotated using gene transcription information from the RefGene database (NCBI). P-values were adjusted using the Benjamini and Hochberg multiple testing procedure. Genes with adjusted p-values < 0.01 were marked as significant. To assess the extent of fun […]

library_books

Aggressive natural killer cell leukemia mutational landscape and drug profiling highlight JAK STAT signaling as therapeutic target

2018
Nat Commun
PMCID: 5908809
PMID: 29674644
DOI: 10.1038/s41467-018-03987-2

[…] pectively, with 63% of the target intervals with sequence coverage being covered by at least 10x (Supplementary Data ).Annotation and filtering of variants was done using the Annovar tool against the RefGene database. Briefly, only variants passing all MuTect2 filters with a TLOD ≥ 6.3 alone or a TLOD ≥ 5.0 and supported by two or more independent COSMIC samples were taken into account. For the tr […]

library_books

Comparative whole genome DNA methylation profiling of cattle sperm and somatic tissues reveals striking hypomethylated patterns in sperm

2018
GigaScience
PMCID: 5928411
PMID: 29635292
DOI: 10.1093/gigascience/giy039

[…] are [] to detect enriched motifs within 1,000 bp up- and downstream of the TSS for genes involved in spermatogenesis. At the same time, the sequences within 1,000 bp up- anddown stream of the TSS for refGene were used as background. We used a website software (Genomatrix, []) to search for TFBS in the Bov-A2 sequence. […]

call_split

RPE phagocytic function declines in age related macular degeneration and is rescued by human umbilical tissue derived cells

2018
J Transl Med
PMCID: 5851074
PMID: 29534722
DOI: 10.1186/s12967-018-1434-6
call_split See protocol

[…] uencing data were processed using ArrayStudio tool (Omicsoft, Cary, NC). Human sequence reads were mapped onto genome assembly GRCh38 (http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/).refGene gene model (http://genome.ucsc.edu/, data created on 2015-07-18) was applied to represent genes in human genomes. TPM (Transcripts Per Million) was applied to calculate gene expression in each […]

library_books

Uncovering the heterogeneous genetic variations in two insulin expressing tumors in a patient with MEN1

2018
PMCID: 5920406
PMID: 29725435
DOI: 10.3892/ol.2018.8184

[…] fied using Strelka (https://sites.google.com/site/strelkasomaticvariantcaller/home) (). The mutational consequences were annotated by ANNOVAR (http://annovar.openbioinformatics.org/) () based on UCSC RefGene. Two calling results were combined, and filtering was performed using an in-house pipeline implemented in Perl. The following filtering criteria were applied: i) Total read count in tumor DNA […]

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