[Arthropod] non-insect-centric arthropod orthology gene sets

Don Gilbert via arthropod%40net.bio.net (by gilbertd from net.bio.net)
Wed Feb 22 14:12:41 EST 2012


Dear arthropodists,

I'm in the process of building and testing a non-insect-centric arthropod
orthology gene set, that includes some transcript assembly for crustaceans
and ticks/Chelicerata.  These I hope to make publicly available this spring.
They are from already published data but the protein genes are
hard to find for some, except the daphnia magna set is not yet
public. These will I think help to place genes of the rest of the
arthropods.

If you have comments/suggestions for this, let me know. 
If in particular you know of public (or soon to be)
"complete" non-insect arthropod gene sets, clue me in.

A few of the transcript-data sets may be too poor to use (I get
only gene fragments, missing many orthologs), except maybe to
pick out a small subset of full genes. It appears currently that
the Chelicerata sets (now ixodes + spidermite, and very poor dog
tick assembly) are all artifactually incomplete, but the union of
these may provide a more complete Chelicerata orthology set.

- Don Gilbert

http://arthropods.eugenes.org/arthropods/orthologs/ARP3x/arpx_summary13d2.txt
======= orthomcl gene groups draft 2 ================

aax13u2omcl/Feb_18

Clade presence for gene families, ncommon gene=24565 
  Clade   Only    Miss    OutAny  OutOnly OutMiss
  Crust   30      538     7033    165     183
  Tick    61      1824    6272    48      566
  inSect  300     3175    6533    114     324
  ----------------------------------------------
  OutAny = 1+ species in clade has outgroup gene family;
  OutOnly= 2+ species in clade have outgroup gene family, none of other clades have.
  OutMiss= no species in clade has outgroup, both other clades have.
  Only = all species in clade have family, none of other clades have
  Miss = no species in clade has family, both other clades have
  Outgroup set is human, zebrafish

Common gene families presence, ncommon=5416, min taxa=9
  Species Have    Miss
  tribol  5223    193
  daphmag 5202    214
  wasp    5192    224
  daphplx 5167    249
  drosmel 5157    259
  human   5110    306
  zfish   5107    309
  aphid   5051    365
  ixodes  4777    639    # so-so incomplete geneset
  tetur   4538    878    # so-so incomplete geneset
  shrimp  4382    1034   # weak,incomplete gene set
  barnacl 3466    1950   # very poor gene set
  dogtick 2328    3088   # very poor gene set
  -----------------------

-- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405
-- gilbertd from indiana.edu--http://marmot.bio.indiana.edu/



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