rnalysis.filtering.CountFilter.find_paralogs_panther

CountFilter.find_paralogs_panther(organism: Union[Literal['auto'], str, int, Literal['Amborella trichopoda', 'Anolis carolinensis', 'Anopheles gambiae', 'Aquifex aeolicus', 'Arabidopsis thaliana', 'Ashbya gossypii', 'Bacillus cereus', 'Bacillus subtilis', 'Bacteroides thetaiotaomicron', 'Batrachochytrium dendrobatidis', 'Bos taurus', 'Brachypodium distachyon', 'Bradyrhizobium diazoefficiens', 'Branchiostoma floridae', 'Brassica napus', 'Brassica rapa subsp. pekinensis', 'Caenorhabditis briggsae', 'Caenorhabditis elegans', 'Candida albicans', 'Canis lupus familiaris', 'Capsicum annuum', 'Chlamydia trachomatis', 'Chlamydomonas reinhardtii', 'Chloroflexus aurantiacus', 'Ciona intestinalis', 'Citrus sinensis', 'Clostridium botulinum', 'Coxiella burnetii', 'Cryptococcus neoformans', 'Cucumis sativus', 'Danio rerio', 'Daphnia pulex', 'Deinococcus radiodurans', 'Dictyoglomus turgidum', 'Dictyostelium discoideum', 'Dictyostelium purpureum', 'Drosophila melanogaster', 'Emericella nidulans', 'Entamoeba histolytica', 'Equus caballus', 'Erythranthe guttata', 'Escherichia coli', 'Eucalyptus grandis', 'Felis catus', 'Fusobacterium nucleatum', 'Gallus gallus', 'Geobacter sulfurreducens', 'Giardia intestinalis', 'Gloeobacter violaceus', 'Glycine max', 'Gorilla gorilla gorilla', 'Gossypium hirsutum', 'Haemophilus influenzae', 'Halobacterium salinarum', 'Helianthus annuus', 'Helicobacter pylori', 'Homo sapiens', 'Hordeum vulgare subsp. vulgare', 'Ixodes scapularis', 'Juglans regia', 'Klebsormidium nitens', 'Korarchaeum cryptofilum', 'Lactuca sativa', 'Leishmania major', 'Leptospira interrogans', 'Listeria monocytogenes', 'Macaca mulatta', 'Manihot esculenta', 'Marchantia polymorpha', 'Medicago truncatula', 'Methanocaldococcus jannaschii', 'Methanosarcina acetivorans', 'Monodelphis domestica', 'Monosiga brevicollis', 'Mus musculus', 'Musa acuminata subsp. malaccensis', 'Mycobacterium tuberculosis', 'Neisseria meningitidis serogroup b', 'Nelumbo nucifera', 'Nematostella vectensis', 'Neosartorya fumigata', 'Neurospora crassa', 'Nicotiana tabacum', 'Nitrosopumilus maritimus', 'Ornithorhynchus anatinus', 'Oryza sativa', 'Oryzias latipes', 'Pan troglodytes', 'Paramecium tetraurelia', 'Phaeosphaeria nodorum', 'Physcomitrella patens', 'Phytophthora ramorum', 'Plasmodium falciparum', 'Populus trichocarpa', 'Pristionchus pacificus', 'Prunus persica', 'Pseudomonas aeruginosa', 'Puccinia graminis', 'Pyrobaculum aerophilum', 'Rattus norvegicus', 'Rhodopirellula baltica', 'Ricinus communis', 'Saccharomyces cerevisiae', 'Salmonella typhimurium', 'Schizosaccharomyces japonicus', 'Schizosaccharomyces pombe', 'Sclerotinia sclerotiorum', 'Selaginella moellendorffii', 'Setaria italica', 'Shewanella oneidensis', 'Solanum lycopersicum', 'Solanum tuberosum', 'Sorghum bicolor', 'Spinacia oleracea', 'Staphylococcus aureus', 'Streptococcus pneumoniae', 'Streptomyces coelicolor', 'Strongylocentrotus purpuratus', 'Sulfolobus solfataricus', 'Sus scrofa', 'Synechocystis', 'Thalassiosira pseudonana', 'Theobroma cacao', 'Thermococcus kodakaraensis', 'Thermodesulfovibrio yellowstonii', 'Thermotoga maritima', 'Tribolium castaneum', 'Trichomonas vaginalis', 'Trichoplax adhaerens', 'Triticum aestivum', 'Trypanosoma brucei', 'Ustilago maydis', 'Vibrio cholerae', 'Vitis vinifera', 'Xanthomonas campestris', 'Xenopus tropicalis', 'Yarrowia lipolytica', 'Yersinia pestis', 'Zea mays', 'Zostera marina', 'helobdella robusta', 'lepisosteus oculatus', 'mycoplasma genitalium']] = 'auto', gene_id_type: Union[str, Literal['auto'], Literal['UniProtKB AC/ID', 'UniParc', 'UniRef50', 'UniRef90', 'UniRef100', 'Gene Name', 'CRC64', 'Ensembl', 'Ensembl Genomes', 'Ensembl Genomes Protein', 'Ensembl Genomes Transcript', 'Ensembl Protein', 'Ensembl Transcript', 'GeneID', 'KEGG', 'PATRIC', 'UCSC', 'WBParaSite', 'WBParaSite Transcript/Protein', 'ArachnoServer', 'Araport', 'CGD', 'ConoServer', 'dictyBase', 'EchoBASE', 'euHCVdb', 'FlyBase', 'GeneCards', 'GeneReviews', 'HGNC', 'LegioList', 'Leproma', 'MaizeGDB', 'MGI', 'MIM', 'neXtProt', 'OpenTargets', 'Orphanet', 'PharmGKB', 'PomBase', 'PseudoCAP', 'RGD', 'SGD', 'TubercuList', 'VEuPathDB', 'VGNC', 'WormBase', 'WormBase Protein', 'WormBase Transcript', 'Xenbase', 'ZFIN', 'eggNOG', 'GeneTree', 'HOGENOM', 'OMA', 'OrthoDB', 'TreeFam', 'CCDS', 'EMBL/GenBank/DDBJ', 'EMBL/GenBank/DDBJ CDS', 'GI number', 'PIR', 'RefSeq Nucleotide', 'RefSeq Protein', 'ChiTaRS', 'GeneWiki', 'GenomeRNAi', 'PHI-base', 'CollecTF', 'BioCyc', 'PlantReactome', 'Reactome', 'UniPathway', 'CPTAC', 'ProteomicsDB']] = 'auto')

Find paralogs within the same species using the PantherDB database.

Parameters

  • organism (str or int) – organism name or NCBI taxon ID of the input genes’ source species.

  • gene_id_type (str or 'auto' (default='auto')) – the identifier type of the genes/features in the FeatureSet object (for example: ‘UniProtKB’, ‘WormBase’, ‘RNACentral’, ‘Entrez Gene ID’). If the annotations fetched from the KEGG server do not match your gene_id_type, RNAlysis will attempt to map the annotations’ gene IDs to your identifier type. For a full list of legal ‘gene_id_type’ names, see the UniProt website: https://www.uniprot.org/help/api_idmapping

Returns

DataFrame describing all discovered paralog mappings.