GenePageReports file descriptions:


1. GenePageGeneralInfo_ManuallyCurated.txt
	File contains general information on all the manually curated gene pages in Xenbase.  
	The file is tab-delimited and has the following format:

	Xenbase gene ID     gene symbol     gene name     gene function     gene synonyms	JGI ID

2. GenePageToJgiTropicalisScaffoldMapping_4.1.txt, GenePageToJgiTropicalisScaffoldMapping_7.1.txt
	File contains a mapping of all Xenbase gene pages to their parent 4.1 JGI models.
	The file is tab-delimited and has the following format:
	
	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
	The file is tab-delimited and has the following format:

	Xenbase gene ID	    gene symbol     NCBI ESTs

	ESTs are presented with the format: accession,evalue.  Each EST is separated by a '|' symbol. 

4. GenePageNcbiEstMapping_tropicalis.txt
	File contains a mapping of NCBI Xenopus tropicalis ESTs to Xenbase gene pages
	The file is tab-delimited and has the following format:

	Xenbase gene ID	    gene symbol     NCBI ESTs

	ESTs are presented with the format: accession,evalue.  Each EST is separated by a '|' symbol. 

5. GenePageAffymetrix_tropicalis1.0.txt
        File contains a mapping of Affymetrix 1.0 expression IDs to Xenbase gene pages
        The file is tab-delimited and has the following format:

        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
        The file is tab-delimited and has the following format:

        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.  The file is tab-delimited and has the following format:

	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  
	The file is tab-delimited and has the following format:

	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     
        The file is tab-delimited and has the following format:

        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.

	The file is tab-delimited and has the following format:
	
	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.
	The file is tab-delimited and has the following format:

	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

13. GeneExpression_tropicalis.txt
	File contains a listing of expression patterns for xenopus tropicalis.
	The file is tab-delimited and has the following format:

	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.
        The file is tab-delimited and has the following format:

	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.
	The file is tab-delimited and has the following format:

	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.
	
	The file is tab-delimited and has the following format:

        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.  The file is in fasta format.
	The fasta header has the following format:

	>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

	The file is tab-delimited and has the following format:

	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

        The file is tab-delimited and has the following format:

        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

        The file is tab-delimited and has the following format:

        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   

        The file is tab-delimited and has the following format:

        gi     accession    Xenbase gene ID     Xenbase gene symbol

22. GenePageGoTerms.txt

	File contains a list of XB-GENEPAGE IDs mapped to GO terms

	The file is tab-delimited and has the following format:

	Xenbase genepage 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

	The file is tab-delimited and has the following format:

	Human Entrez Gene ID	Xenbase genepage ID	Xenbase gene symbol	Xenbase gene name

24. XenbaseGeneMouseOrthologMapping.txt

        File contains a mapping of XB-GENEPAGE IDs and annotation to mouse Entrez Gene IDs

        The file is tab-delimited and has the following format:

        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

        The file is tab-delimited and has the following format:

        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.

	The file is tab-delimited and has the following format:

	XB-GENEPAGE ID     XB-GENE IDs for tropicalis and laevis

	The XB-GENE IDs are comma-separated

27. JgiToXenbaseGenePage_4.1.txt, JgiToXenbaseGenePage_7.1.txt

	File contains the mapping JGI tropicalis models to Xenbase gene page IDs.

	The file is tab-delimited and has the following format:

	model name     Xenbase tropicalis gene ID     gene symbol     gene name 
