GenePageReports file descriptions:
 FTP_FILE_INVENTORY
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 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   
CSV   
OmimDataDump.pl perl   
XB Umbrella Gene 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) 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      

 46) 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
