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.