WormBase Tree Display for Analysis: Tabach et al., 2013 Correlated conservation

Tabach et al., 2013 Correlated conservation Based_on_WB_Release: 220
  Description: The phylogenetic profiles of approximately 20,000 C. elegans proteins was determined in 85 genomes, representing diverse taxa of the eukaryotic tree of life: 33 animals, 6 land plants, 1 alga, 31 Ascomycota fungi, 3 Basidiomycota fungi and 12 protists. A Bayesian approach was used to integrate the phylogenetic profile analysis with predictions from diverse transcriptional coregulation and proteome interaction data sets to assign a probability for each protein for a role in a small RNA pathway. A non-binary method of phylogenetic profiling was developed and used to cluster all protein sequences encoded by C. elegans genes. BLAST scores were normalized to the length of the query sequence and for relative phylogenetic distance between C. elegans and the queried organism. The matrix of 864,644 conservation scores for the 10,054 C. elegans proteins in the 86 genomes was queried either with a single protein to generate a ranking of other C. elegans proteins with the most similar pattern of conservation values or using a more global hierarchical clustering method. Correlation coefficients were calculated using the normalized phylogenetic profile matrix (NPP) and genes were rank ordered.
  Species_in_analysis: Caenorhabditis elegans
    Caenorhabditis briggsae
    Pristionchus pacificus
    Caenorhabditis brenneri
    Caenorhabditis remanei
    Caenorhabditis japonica
    Saccharomyces cerevisiae
    Mus musculus
    Homo sapiens
    Danio rerio
    Aedes aegypti
    Ajellomyces dermatitidis
    Anolis carolinensis
    Anopheles gambiae
    Arabidopsis thaliana
    Aspergillus clavatus
    Aspergillus flavus
    Aspergillus niger
    Aspergillus oryzae
    Aspergillus terreus
    Babesia bovis
    Botryotinia fuckeliana
    Candida albicans
    Candida glabrata
    Canis familiaris
    Chaetomium globosum
    Chlamydomonas reinhardtii
    Ciona intestinalis
    Ciona savignyi
    Clavispora lusitaniae
    Coprinopsis cinerea
    Cryptosporidium parvum
    Dasypus novemcinctus
    Debaryomyces hansenii
    Dictyostelium discoideum
    Dipodomys ordii
    Drosophila melanogaster
    Entamoeba histolytica
    Felis catus
    Gallus gallus
    Gasterosteus aculeatus
    Gibberella zeae
    Ixodes scapularis
    Kluyveromyces lactis
    Leishmania major
    Lodderomyces elongisporus
    Malassezia globosa
    Neosartorya fischeri
    Neurospora crassa
    Ornithorhynchus anatinus
    Oryza sativa
    Oryzias latipes
    Pan troglodytes
    Paracoccidioides brasiliensis
    Pediculus humanus
    Penicillium chrysogenum
    Phaeodactylum tricornutum
    Phaeosphaeria nodorum
    Plasmodium falciparum
    Plasmodium vivax
    Podospora anserina
    Populus trichocarpa
    Pteropus vampyrus
    Rattus norvegicus
    Schizosaccharomyces japonicus
    Schizosaccharomyces pombe
    Sclerotinia sclerotiorum
    Sorghum bicolor
    Taeniopygia guttata
    Takifugu rubripes
    Tetraodon nigroviridis
    Thalassiosira pseudonana
    Theileria annulata
    Trypanosoma brucei
    Tursiops truncatus
    Vitis vinifera
    Xenopus tropicalis
    Yarrowia lipolytica
    Zygosaccharomyces rouxii
    Filobasidiella neoformans
    Arthroderma otae
    Uncinocarpus reesii
    Lachancea thermotolerans
    Scheffersomyces stipitis
    Brachypodium distachyon
    Giardia intestinalis
  Reference: WBPaper00041947