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Index of /release1/dpulex_jgi060905/gene-evidence

      Name                                   Last modified       Size  Description

[DIR] Parent Directory 09-Apr-2019 09:22 - [TXT] dpulex-geneevd-venn.info 03-Apr-2009 18:12 3k [   ] dpulex-genevd-venn4d.pdf 03-Apr-2009 17:26 27k [IMG] dpulex-genevd-venn4d.png 03-Apr-2009 17:36 116k [TXT] dpulex_JGI_V11.allevd.idtab 03-Apr-2009 14:37 3.0M [TXT] dpulex_JGI_V11.arp08.ids 04-Apr-2009 18:41 1.0M [TXT] dpulex_JGI_V11.dmagna.ids 02-Nov-2008 19:36 400k [TXT] dpulex_JGI_V11.gene.ids 02-Nov-2008 19:47 691k [TXT] dpulex_JGI_V11.kogall07.ids 03-Apr-2009 14:13 444k [TXT] dpulex_JGI_V11.nrprot0903b_an05.ids 04-Apr-2009 13:22 1.7M [TXT] dpulex_JGI_V11.omcl.ids 04-Apr-2009 17:25 453k [TXT] dpulex_JGI_V11.pasa_est.ids 02-Nov-2008 19:36 206k [TXT] dpulex_JGI_V11.protspec.ids 25-Mar-2009 20:00 33k [TXT] dpulex_JGI_V11.tar80.ids 04-Apr-2009 13:50 429k [TXT] dpulex_JGI_V11.tilemaxa2.ids 03-Apr-2009 14:26 302k [   ] evd5annot.tab.old.gz 25-Mar-2009 21:16 1.3M [TXT] table.s10.daphnia_gene_evidence.txt 04-Apr-2009 18:50 6.4M [TXT] table.s11.daphnia_targene_evidence.txt 04-Apr-2009 17:13 429k


The table table.s10.daphnia_gene_evidence.txt
has evidence columns for each daphnia JGI_V11 gene (30,900 rows),
including those 4,040 with no evidence at criteria.
Evidence includes Expression as EST and tile TAR matches,
other species orthology gene IDs, descriptions and scores.

The table.s11.daphnia_targene_evidence.txt has more limited evidence
for tile expression TAR-genes.

THe dpulex_JGI_V11.*.ids files have just one line of evidence,
just the gene IDs and type-column, suited for venn counts.

- Don Gilbert, March/April 2009

% wc -l dpulex_JGI_V11.*.ids   
   30940 dpulex_JGI_V11.gene.ids	:: all gene ids
   15139 dpulex_JGI_V11.arp08.ids	:: Orthologs from eugenes/Arthropod OrthoMCL aug 2008 analysis
   18765 dpulex_JGI_V11.dmagna.ids      :: Daphnia magna matches
   15806 dpulex_JGI_V11.kogall07.ids    :: JGI KOG orthologs from 2007
   17286 dpulex_JGI_V11.nrprot0903b_an05.ids  :: NCBI NR orthologs (p<1e-5) as of 2009-March
   13976 dpulex_JGI_V11.omcl.ids        :: D. pulex paralogs
   10578 dpulex_JGI_V11.pasa_est.ids    :: est assemblies
    1399 dpulex_JGI_V11.protspec.ids    :: proteomics
   14142 dpulex_JGI_V11.tar80.ids       :: tile TAR 80% overlap
   11969 dpulex_JGI_V11.tilemaxa2.ids   :: max expression >= 2 log above background

Some counts are: 
   Only homology data: 23239 genes
   Only expressed Tile + EST : 18451 genes
   Any evidence : 27090 (including paralogs)
   Any but paralog: 25690
   Any but paralog or tile : 24171