Diff for "HumanGeneStatistics"

Differences between revisions 2 and 3

Gene, GeneOntology를 이용한 유전자에 관한 다양한 통계들.

재료

Gene: NCBI gene ftp - Homo_sapiens_gene_info.gz (2012-06-28)
GO: Gene ontology site - GO.obo (2012-06-28)
GOA: NCBI gene ftp - gene2go (2012-06-28)

Count

Gene: Gene.objects.count() (->) 43,484
GO: GOTerm.objects.count() (->) 35,847
GOA: GOAssociation.objects.count() (->) 190,477

Gene category

Protein coding: 20,258
rRNA: 478
snRNA: 96
unknown: 2,954
scRNA: 5
pseudo: 12,671
other: 817
miscRNA: 5,219
tRNA: 599
snoRNA: 391
ncRNA: 1

chromosome 별 유전자 갯수

   1 >>> chrs = defaultdict(int)
   2 >>> for gene in Gene.objects.all():
   3         chrs[gene.chromosome] += 1
   4 >>> sorted(chrs.items(), key=itemgetter(0))
   5 [(u'-', 458),
   6  (u'1', 4001),
   7  (u'10', 1606),
   8  (u'10|19|3', 1),
   9  (u'11', 2514),
  10  (u'12', 1960),
  11  (u'12|Un', 1),
  12  (u'13', 1119),
  13  (u'13|Un', 1),
  14  (u'14', 1704),
  15  (u'15', 1458),
  16  (u'16', 1546),
  17  (u'17', 2062),
  18  (u'17|Un', 1),
  19  (u'18', 686),
  20  (u'18|Un', 2),
  21  (u'19', 2267),
  22  (u'2', 2795),
  23  (u'20', 1024),
  24  (u'21', 543),
  25  (u'22', 1004),
  26  (u'2|Un', 1),
  27  (u'3', 2303),
  28  (u'3|11', 1),
  29  (u'3|Un', 5),
  30  (u'4', 1694),
  31  (u'5', 1900),
  32  (u'6', 2437),
  33  (u'7', 2248),
  34  (u'8', 1574),
  35  (u'9', 1756),
  36  (u'MT', 74),
  37  (u'Un', 205),
  38  (u'X', 2015),
  39  (u'X|Y', 33),
  40  (u'Y', 485)]

Checks

Gene parsing시 chromosome 정리

-  ⇤ ← Revision 2 as of 2012-07-08 08:29:22 → 
  Size: 436
  Editor: 221
  Comment: it's only for human
+   ← Revision 3 as of 2012-07-08 08:48:02 → ⇥
  Size: 1483
  Editor: 221
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 13:
+Gene category
 * Protein coding: 20,258
 * rRNA: 478
 * snRNA: 96
 * unknown: 2,954
 * scRNA: 5
 * pseudo: 12,671
 * other: 817
 * miscRNA: 5,219
 * tRNA: 599
 * snoRNA: 391
 * ncRNA: 1

chromosome 별 유전자 갯수

{{{#!python
>>> chrs = defaultdict(int)
>>> for gene in Gene.objects.all():
        chrs[gene.chromosome] += 1
>>> sorted(chrs.items(), key=itemgetter(0))
[(u'-', 458),
 (u'1', 4001),
 (u'10', 1606),
 (u'10|19|3', 1),
 (u'11', 2514),
 (u'12', 1960),
 (u'12|Un', 1),
 (u'13', 1119),
 (u'13|Un', 1),
 (u'14', 1704),
 (u'15', 1458),
 (u'16', 1546),
 (u'17', 2062),
 (u'17|Un', 1),
 (u'18', 686),
 (u'18|Un', 2),
 (u'19', 2267),
 (u'2', 2795),
 (u'20', 1024),
 (u'21', 543),
 (u'22', 1004),
 (u'2|Un', 1),
 (u'3', 2303),
 (u'3|11', 1),
 (u'3|Un', 5),
 (u'4', 1694),
 (u'5', 1900),
 (u'6', 2437),
 (u'7', 2248),
 (u'8', 1574),
 (u'9', 1756),
 (u'MT', 74),
 (u'Un', 205),
 (u'X', 2015),
 (u'X|Y', 33),
 (u'Y', 485)]
}}}




Checks
 * Gene parsing시 chromosome 정리