PhenoGen Informatics
The site for quantitative genetics of the transcriptome.
Important Update: Due to the high costs of maintaining PhenoGen.org, we are phasing out most of the site's functionality.
HRDP Data downloads and the REST API will remain active and fully supported. If you found other parts of the site helpful for your work, please email us at info@phenogen.org.

PhenoGen Website Version

Version:   3.8.0
Last updated:   2022-09-21 00:00:00



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 1.12.0 and Database version 2.3

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 v111,Rn6-Ensembl v105, except Rn5-v79
  • RefSeq(source:UCSC Genome Browser): Downloaded 2/2022 except rn6- ,rn5 - 7/2015


Annotations/Gene ID Matching

iDecoder:   Last updated on February 25th, 2022 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 v105
  • FlyBase gene_map_table_fb_2022_01.tsv file and fbgn_NAseq_Uniprot_fb_2021_01.tsv
  • MGI database links file generated from the ACC_Accession table on 2/25/2022
  • MGI_Coordinate.rpt links file, downloaded 2/25/2022
  • NCBI gene2accession file, downloaded 2/25/2022
  • NCBI gene2unigene file, downloaded 2/25/2022
  • NCBI gene_info file, downloaded 2/25/2022
  • NCBI homologene.data file, downloaded 2/25/2022
  • RGD GENES file, last updated on 2/25/2022
  • SwissProt uniprot_sprot.dat file, last updated on 2/25/2022
  • PhenoGen Merged Transcriptome v6 with known gene/transcript annotation from Ensembl v105.