News for Chimpanzee Ensembl Release 89 (May 2017)

Microarray Probe Mapping Update

Update microarray probe mappings for all arrays of all species

Map array probes onto 15 mouse strains

Map array probes onto the below mouse strains:

mus_musculus_129s1svimj
mus_musculus_aj
mus_musculus_akrj
mus_musculus_balbcj
mus_musculus_c3hhej
mus_musculus_c57bl6nj
mus_musculus_casteij
mus_musculus_cbaj
mus_musculus_dba2j
mus_musculus_fvbnj
mus_musculus_lpj
mus_musculus_nodshiltj
mus_musculus_nzohlltj
mus_musculus_pwkphj
mus_musculus_wsbeij

ncRNAtrees and homologies

• Classification based on Rfam models (v12.1)
• Multiple sequence alignments with Infernal
• Phylogenetic reconstruction using RAxML
• Phylogenetic reconstruction using FastTree2 and ExaML for very big families
• Additional multiple sequence alignments with Prank (w/ genomic flanks)
• Additional phylogenetic reconstruction using PhyML and NJ
• Phylogenetic tree merging using TreeBeST
• Per family gene dynamics using CAFE
• Homology inference
• Secondary structure plots

patch_88_89_a.sql - Schema version update

88 -> 89

Protein Families

Updated HMM families including all Ensembl transcript isoforms (including human non-reference haplotypes) and newest Uniprot Metazoa.

 -- Clustering by PantherScore (based on Ensembl HMM library)
 -- Multiple Sequence Alignments with MAFFT (v.7.221)

ProteinTrees and homologies

GeneTrees (protein-coding) with new/updated genebuilds and assemblies

 -- all-vs-all blastp (ncbi-blast-2.2.30+)
 -- Clustering using hcluster_sg
 -- Multiple sequence alignments using MCoffee (Version_9.03.r1318) or Mafft (mafft-7.221)
 -- Phylogenetic reconstruction using TreeBeST
 -- Homology inference
 -- Pairwise gene-based dN/dS scores for high coverage species pairs only (both on orthologues and paralogues) (codeml/PAML v4.3)
 -- GeneTree stable ID mapping
 -- Per family gene dynamics using CAFE (v2.2)

 -- computation of pairwise gene-order conservation score

 -- comparison of orthologies with whole-genome alignments

 -- high-confidence calls

GO terms for transcripts

GO terms have been introduced for some miRNAs. As a result, GO terms are now linked to transcripts rather than translations.

Database schema changes

patch_88_89_a - Schema change

patch_88_89_b - Create table probe_seq

patch_88_89_c - Create table probe_feature_transcript

patch_88_89_d - Create table probe_transcript

patch_88_89_e - Create table probe_set_transcript

patch_88_89_f  - Remove probe features from object_xref and xref table

patch_88_89_g - Remove probe mappings from the xref tables

patch_88_89_h - Remove probe set mappings from the xref tables.

patch_88_89_i - Add link columns to array table 

patch_88_89_j - Added array_chip_id column to probe_set table

patch_88_89_k - Added probe_seq_id column to probe table

Deprecate methods

The following methods have been deprecated and will be removed in Ensembl release 93
Bio::EnsEMBL::Funcgen::Epigenome::tissue()
Bio::EnsEMBL::Funcgen::Epigenome::ontology_accession()

Ensembl 89 mart databases

• Ensembl Genes 89
  • Updated Microarray probes/probesets for all the species
  • Dataset "meugenii_gene_ensembl" was renamed to "neugenii_gene_ensembl"
  • Dataset "tsyrichta_gene_ensembl" was renamed to "csyrichta_gene_ensembl"
  • GO and GOSlim terms were moved from Translation to Transcript
• Mouse Genes 89
  • Microarray probes/probesets added for all the mouse strains
  • GO and GOSlim terms were moved from Translation to Transcript
• Ensembl Variation 89
  • New filters for regulatory and motif consequence types
• Ensembl Regulation 89
  • Updated VISTA Enhancers for human and mouse

Phenotype data updates

• Updated Human phenotype data from different sources including NHGRI-EBI GWAS, OMIM, ClinVar, UniProt, Cosmic Gene Census, DDG2P, MIM Morbid and Orphanet.
• OMIA data for several species
• AnimalQTL data for several species
• RGD data for Rat
• ZFIN data for Zebrafish
• IMPC data for Mouse
• MGI data for Mouse

strain_gtype_poly table to be dropped

The strain_gtype_poly table will be dropped.