PhenoGen Informatics
The site for quantitative genetics of the transcriptome.

Summer of Rat Genomics and Genetics Workshop - Aug 2nd-3rd, 2019 - Colorado - NIDA Center for Omics, Systems Genetics and the Addictome
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PhenoGen Website Version

Version:   3.5.0
Last updated:   2018-11-19 00:00:00.0



Tools Used on This Website

Promoter (oPOSSUM):   version 2.0

Promoter (MEME):   version 4.10 patch 4

R:  version 3.4.1

BioConductor:  version 3.0

multiMiR:  version 1.0

CIRCOS:  version 0.69-4

D3js:  version 4.8

jQuery & jQuery UI:  version 1.11.2 and 1.11.3



Genome Data Browser Annotations

  • Ensembl v93, except Rn5-v79
  • RefSeq(source:UCSC Genome Browser): Downloaded 9/2018 except rn5 - 7/2015


Annotations/Gene ID Matching

iDecoder:   Last updated on February 16th, 2018 with annotation data from the following sources:

  • Annotation file for Affymetrix Genechip Drosophila Genome [DrosGenome1] na32
  • Annotation file for Affymetrix GeneChip Human Genome U133 Plus 2.0[HG-U133_Plus_2], na32
  • Annotation file for Affymetrix Genechip Mouse Exon 1.0 ST Array, na32
  • Annotation file for Affymetrix GeneChip Mouse Expression Array MOE430A [MOE430A], na32
  • Annotation file for Affymetrix GeneChip Mouse Expression Array MOE430B [MOE430B], na32
  • Annotation file for Affymetrix GeneChip Mouse Genome 430A 2.0 [Mouse430A_2], na32
  • Annotation file for Affymetrix GeneChip Mouse Genome 430 2.0 [Mouse430_2], na32
  • Annotation file for Affymetrix Genechip Murine Genome U74A [MG_U74A], na20
  • Annotation file for Affymetrix Genechip Murine Genome U74Av2 [MG_U74Av2], na22
  • Annotation file for Affymetrix Genechip Murine Genome U74Bv2 [MG_U74Bv2], na22
  • Annotation file for Affymetrix Genechip Murine Genome U74Cv2 [MG_U74Cv2], na22
  • Annotation file for Affymetrix Genechip Rat Exon 1.0 ST Array, na32
  • Annotation file for Affymetrix GeneChip Rat Expression Array RAE230A [RAE230A], na32
  • Annotation file for Affymetrix Genechip Rat Genome U34A [RG_U34A], na32
  • Annotation file for Amersham Codelink UniSet Mouse I
  • Annotation file for Codelink Rat Whole Genome
  • Annotation file for Codelink Mouse Whole Genome
  • Location data from Ensembl for Mouse, Human, and Rat from Ensembl Genes v93
  • FlyBase gene_map_table_fb_2017_06.tsv file and fbgn_NAseq_Uniprot_fb_2017_06.tsv
  • MGI database links file generated from the ACC_Accession table on 1/29/2018
  • MGI_Coordinate.rpt links file, downloaded 1/29/2018
  • NCBI gene2accession file, downloaded 1/29/2018
  • NCBI gene2unigene file, downloaded 1/29/2018
  • NCBI gene_info file, downloaded 1/29/2018
  • NCBI homologene.data file, downloaded 1/29/2018
  • RGD GENES file, last updated on 1/29/2018
  • SwissProt uniprot_sprot.dat file, last updated on 1/29/2018
  • PhenoGen Merged Transcriptome v1 with known gene/transcript annotation from Ensembl v93.