GenePageReports file descriptions: FTP_FILE_INVENTORY ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1) GenePageGeneralInfo_ManuallyCurated.txt File contains general information on all the manually curated gene pages in Xenbase. TSV XenbaseGenePageDump.pl perl Xenbase gene ID|gene symbol|gene name|gene function|gene synonyms 2) GenePageToJgiTropicalisScaffoldMapping_4.1.txt File contains a mapping of all Xenbase gene pages to their parent 4.1 JGI models TSV GenePageJgiDataMapping.pl perl Xenbase gene ID|gene symbol|JGI Model Name|JGI Scaffold Name|JGI Scaffold Start Position|JGI Scaffold End Position|JGI Scaffold Strand 3) GenePageNcbiEstMapping_laevis.txt File contains a mapping of NCBI Xenopus laevis ESTs to Xenbase gene pages TSV GenePageNcbiEstMapping.pl perl Xenbase gene ID|gene symbol|NCBI ESTs ESTs are presented with the format: accession,evalue. Each EST is separated by a | pipe symbol. 4) GenePageNcbiEstMapping_tropicalis.txt File contains a mapping of NCBI Xenopus tropicalis ESTs to Xenbase gene pages TSV GenePageNcbiEstMapping.pl perl Xenbase gene ID|gene symbol|NCBI ESTs ESTs are presented with the format: accession,evalue. Each EST is separated by a | pipe symbol. 5) GenePageAffymetrix_tropicalis1.0.txt File contains a mapping of Affymetrix 1.0 expression IDs to Xenbase gene pages TSV GenePageAffymetrixMapping.pl perl Xenbase gene ID|gene symbol|Affymetrix IDs Affymetrix IDs for a given gene page are comma-separated 6) GenePageAffymetrix_laevis1.0.txt File contains a mapping of Affymetrix 1.0 expression IDs to Xenbase gene pages TSV GenePageAffymetrixMapping.pl perl Xenbase gene ID|gene symbol|Affymetrix IDs Affymetrix IDs for a given gene page are comma-separated 7) GenePageInteractants.txt File contains a list of gene interactants for each gene page in Xenbase based on co-citation in the literature. TSV GenePageInteractantsMapping.pl perl Xenbase gene ID|gene symbol|interactant|ID:interactant symbol:co-citation occurrence Interactants for a given gene page are comma-separated 8) GenePageTropicalisEntrezGeneUnigeneMapping.txt File contains a mapping of Xenopus tropicalis NCBI Entrez Gene and Unigene IDs for each gene page in Xenbase TSV GenePageEntrezGeneUnigeneMapping.pl perl Xenbase gene ID|gene symbol|Entrez Gene ID|Unignene ID 9) GenePageLaevisEntrezGeneUnigeneMapping.txt File contains a mapping of Xenopus laevis NCBI Entrez Gene and Unigene IDs for each gene page in Xenbase TSV GenePageEntrezGeneUnigeneMapping.pl perl Xenbase gene ID|gene symbol|Entrez Gene ID|Unignene ID 10) GenePageAnatomyOntologyMapping.txt File contains a mapping of Xenbase gene pages to Xenopus Anatomy Ontology (XAO) development stages and tissues. The anatomy data is pooled from the tropicalis and laevis frog species. Expression data is obtained from cDNA libraries as well as images from large scale screens, community submissions and publications TSV GenePageAnatomyOntologyMapping.pl perl Xenbase gene ID|gene symbol|start stage|end stage|tissues Stage information is provided as a range from the earliest point of expression to the latest Tissues are provided as a comma-separated list 11) GenePageEnsemblModelMapping.txt File contains a mapping of Xenbase gene pages to Ensembl Xentr4.1 models. TSV EnsemblGenePageMapping.pl perl Xenbase gene ID|gene symbol|Ensembl model name 12) XenbaseGeneModels.gff3.gz All of the Xenopus tropicalis genemodels from Xentr 4.1 dumped out in GFF3 format GFF3 ChadoGeneModelsToGff3.pl perl 13) GeneExpression_tropicalis.txt File contains a listing of expression patterns for xenopus tropicalis. TSV GenePageExpressionDump.pl perl Xenbase gene ID|gene symbol|genotype|anatomical tissue|start stage|end stage|assay|evidence ID(image ID)|experiment ID|literature ID|source|curation status Note that the fields 'anatomical tissue', 'start stage' and 'end stage' are of the format 'XAO_ID XAO_Name' 14) GeneExpression_laevis.txt File contains a listing of expression patterns for xenopus laevis. TSV GenePageExpressionDump.pl perl Xenbase gene ID|gene symbol|genotype|anatomical tissue|start stage|end stage|assay|evidence ID(image ID)|experiment ID|literature ID|source|curation status Note that the fields 'anatomical tissue', 'start stage' and 'end stage' are of the format 'XAO_ID XAO_Name' 15) TropicalisGenePages_NoModel.txt File contains a listing of Xenbase gene pages created using an NCBI xenopus tropicalis Entrez Gene entry as a seed. These gene pages have no genomic gene model associated with them. These models will contain, where applicable, xenopus laevis gene data. TSV DumpTropNonModelGenes.pl perl Xenbase gene ID|gene symbol|tropicalis unigene ID|tropicalis Entrez Gene ID 16) LaevisGenePages_NoModel.txt File contains a listing of Xenbase gene pages created using an NCBI xenopus laevis Entrez Gene entry as a seed. These pages have no genomic gene model and no corresponding xenopus tropicalis genetic data associated with them. TSV DumpLaevisNonModelGenes.pl perl Xenbase gene ID|gene symbol|laevis unigene ID|laevis Entrez Gene ID 17) XenbaseGenePage_JgiModel_Transcripts.gz File contains a list of JGI 4.1 transcript sequences associated with Xenbase gene pages. fasta JgiGenemodelTranscriptDump.pl perl >JGI transcript ID|JGI model name|Xenbase gene page ID|Xenbase gene page symbol 18) NcbiProteinXenbaseGene_tropicalis.txt File contains a list of NCBI tropicalis proteins mapped to the appropriate Xenbase genepage ID TSV UniprotDump.pl perl gi|accession|Xenbase gene ID|Xenbase gene symbol 19) NcbiProteinXenbaseGene_laevis.txt File contains a list of NCBI laevis proteins mapped to the appropriate Xenbase genepage ID TSV NcbiGenePageDump.pl perl gi|accession|Xenbase gene ID|Xenbase gene symbol 20) NcbiMrnaXenbaseGene_tropicalis.txt File contains a list of NCBI tropicalis mRNAs mapped to the appropriate Xenbase genepage ID. TSV XenopusNcbiSequence.pl perl gi|accession|Xenbase gene ID|Xenbase gene symbol 21) NcbiMrnaXenbaseGene_laevis.txt File contains a list of NCBI laevis mRNAs mapped to the appropriate Xenbase genepage ID TSV NcbiSequenceXenbaseGeneMapping.pl perl gi|accession|Xenbase gene ID|Xenbase gene symbol 22) GeneGoTerms.txt File contains a list of XB-GENE IDs mapped to GO terms TSV GeneGoTerms.pl perl Xenbase gene ID|gene symbol|GO Ids The list of GO IDs is comma separated 23) XenbaseGeneHumanOrthologMapping.txt File contains a mapping of XB-GENEPAGE IDs and annotation to human Entrez Gene IDs TSV MapXenbaseGenesToOrthologEntrez.pl perl Human Entrez Gene ID|Xenbase genepage ID|Xenbase gene symbol|Xenbase gene name 24) XenbaseGeneMouseOrthologMapping.txt ile contains a mapping of XB-GENEPAGE IDs and annotation to mouse Entrez Gene IDs TSV MapXenbaseGenesToOrthologMODs.pl perl Mouse Entrez Gene ID|Xenbase genepage ID|Xenbase gene symbol|Xenbase gene name 25) XenbaseGeneZebrafishOrthologMapping.txt File contains a mapping of XB-GENEPAGE IDs and annotation to zebrafish Entrez Gene IDs TSV MapXenbaseGenesToOrthologMODs.pl perl Zebrafish Entrez Gene ID|Xenbase genepage ID|Xenbase gene symbol|Xenbase gene name 26) XenbaseGenepageToGeneIdMapping.txt File contains the mapping of XB-GENEPAGE IDs, the primary identifier for a genepage to XB-GENE IDs for individual tropicalis and laevis genes. TSV XenbaseGenepageToGeneIdMapping.pl perl XB-GENEPAGE ID|XB-GENE IDs for tropicalis and laevis The XB-GENE IDs are comma-separated 27) JgiToXenbaseGenePage_4.1.txt File contains the mapping JGI tropicalis models to Xenbase gene page IDs. TSV JgiGenePageDump.pl perl model name|Xenbase tropicalis gene ID|gene symbol|gene name 28) JgiToXenbaseGenePage_7.1.txt File contains the mapping JGI tropicalis models to Xenbase gene page IDs. TSV JgiGenePageDump.pl perl model name|Xenbase tropicalis gene ID|gene symbol|gene name 29) GenePageToJgiTropicalisScaffoldMapping_7.1.txt File contains a mapping of all Xenbase gene pages to their parent 7.1 JGI models TSV GenePageJgiDataMapping.pl perl Xenbase gene ID|gene symbol|JGI Model Name|JGI Scaffold Name|JGI Scaffold Start Position|JGI Scaffold End Position|JGI Scaffold Strand 30) GeneExpPerTissue_laevis.txt File contains a listing of expression patterns for xenopus laevis. TSV GenePageExpPerTissueDump.pl perl col_speciesGeneId|col_speciesGeneSymbol|col_wildType|col_anatomyXaoId col_anatomyItem|col_startStageXaoId col_startStage|col_endStageXaoId col_endStage|col_experiment|XB-IMG-col_imageId|XB-EXP-col_experimentId|col_source|XB-ART-col_xenPaperId|col_annotStatus Note that the fields 'anatomical tissue', 'start stage' and 'end stage' are of the format 'XAO_ID XAO_Name' 31) GeneExpPerTissue_tropicalis.txt File contains a listing of expression patterns for xenopus laevis. TSV GenePageExpPerTissueDump.pl perl col_speciesGeneId|col_speciesGeneSymbol|col_wildType|col_anatomyXaoId col_anatomyItem|col_startStageXaoId col_startStage|col_endStageXaoId col_endStage|col_experiment|XB-IMG-col_imageId|XB-EXP-col_experimentId|col_source|XB-ART-col_xenPaperId|col_annotStatus Note that the fields 'anatomical tissue', 'start stage' and 'end stage' are of the format 'XAO_ID XAO_Name' 32) GenePageAffymetrix_laevis2.0.txt File contains a mapping of Affymetrix 2.0 expression IDs to Xenbase gene pages TSV GenePageAffymetrixMapping.pl perl Xenbase gene ID|gene symbol|Affymetrix IDs Affymetrix IDs for a given gene page are comma-separated 33) GenePageToJgiTropicalisScaffoldMapping_8.0.txt File contains a mapping of all Xenbase gene pages to their parent 8.0 JGI models TSV GenePageJgiDataMapping.pl perl Xenbase gene ID|gene symbol|JGI Model Name|JGI Scaffold Name|JGI Scaffold Start Position|JGI Scaffold End Position|JGI Scaffold Strand 34) GenePageToJgiLaevisScaffoldMapping_6.0.txt File contains a mapping of all Xenbase gene pages to their parent 6.0 JGI models TSV GenePageJgiDataMapping.pl perl Xenbase gene ID|gene symbol|JGI Model Name|JGI Scaffold Name|JGI Scaffold Start Position|JGI Scaffold End Position|JGI Scaffold Strand 35) GenePageToJgiLaevisScaffoldMapping_7.1.txt File contains a mapping of all Xenbase gene pages to their parent 7.1 JGI models TSV GenePageJgiDataMapping.pl perl Xenbase gene ID|gene symbol|JGI Model Name|JGI Scaffold Name|JGI Scaffold Start Position|JGI Scaffold End Position|JGI Scaffold Strand 36) GenePageToJgiLaevisScaffoldMapping_8.0.txt File contains a mapping of all Xenbase gene pages to their parent 8.0 JGI models TSV GenePageJgiDataMapping.pl perl Xenbase gene ID|gene symbol|JGI Model Name|JGI Scaffold Name|JGI Scaffold Start Position|JGI Scaffold End Position|JGI Scaffold Strand 37) InSituHybridization_laevis.txt File contains a mapping of all Xenbase gene pages with stage, image and curation method TSV InSituGeneProfileDump.pl perl Xenbase gene ID|gene symbol|StartStage|EndStage|XenbaseImage|CurationMethod 38) InSituHybridization_tropicalis.txt File contains a mapping of all Xenbase gene pages with stage, image and curation method TSV InSituGeneProfileDump.pl perl Xenbase gene ID|gene symbol|StartStage|EndStage|XenbaseImage|CurationMethod 39) JgiToXenbaseGenePage_8.0.txt File contains the mapping JGI tropicalis models to Xenbase gene page IDs. TSV JgiGenePageDump.pl perl model name|Xenbase tropicalis gene ID|gene symbol|gene name 40) LiteratureMatchedGenesByPaper.txt NA TSV LiteratureMatchedGenesByPaper.pl perl Article|pubMedID|genePageId_and_Symbol genePageId_and_Symbol listing comma separated 41) Trop4.1EnsemblToHumanEnsemblMapping.txt NA TSV NA perl NA 42) TropicalisGenePage_NoModel.fasta File contains a listing of Xenbase gene pages created using an NCBI xenopus tropicalis Entrez Gene entry as a seed. These gene pages have no genomic gene model associated with them. These models will contain, where applicable, xenopus laevis gene data. fasta DumpTropNonModelGenes.pl perl Xenbase gene ID|gene symbol|tropicalis unigene ID|tropicalis Entrez Gene ID 43) XenbaseGeneNonEntrezOrthologMapping.txt File contains a listing of Xenbase gene pages with OMIM, ZFIN, MGI and GEISHA TSV MapXenbaseGenesToOrthologs.pl perl Xenbase|OMIM|MGI|ZFIN|GEISHA 44) XenbaseOmimData.txt File contains a listing of Xenbase gene pages with OMIM gene, disease and laevis and trop identifiers TSV OmimDataDump.pl perl XB GenePage ID|Gene Symbol|Human Entrez ID|OMIM Gene ID|OMIM Disease IDs(|)|XB tropicalis ID|Entrez tropicalis ID|XB laevis.L ID|laevis.L Symbol|Entrez laevis.L ID|XB laevis.S ID|laevis.S Symbol|Entrez laevis.S ID 45) XenbaseDiseaseOntologyData.txt File contains a listing of Xenbase gene pages with Disease Ontology IDs and names TSV DODataDump.pl perl XB GenePage ID|Gene Symbol|DOID - name(|) 46) GeneKoTerms.txt File contains a list of XB-GENE IDs mapped to KEGG terms TSV GeneKoTerms.pl perl Xenbase gene ID|gene symbol|KEGG Ids The list of KEGG IDs is comma separated 47) GeneExternalRef.txt File contains a list of XB-GENE IDs with external entities TSV GeneExternalRef.pl perl Xenbase gene ID|gene symbol|gene name|NCBI taxon ID|Entrez ID|JGI IDs (delimited)|Uniprot IDs (delimited)|ENSEMBL IDs (delimited) The list of IDs is pipe delimited