Athurva Gore/LabNotes/ExomeReseq/2009-5-13: Difference between revisions

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  ILMN_1753648 tripartite motif-containing 51 RG Homo sapiens
  ILMN_1753648 tripartite motif-containing 51 RG Homo sapiens
* GO Terms associated with this set:
* GO Terms associated with this set:
  Category Term Count % PValue Genes List Total Pop Hits Pop Total Fold Enrichment Bonferroni Benjamini FDR
  Category   Term
  UP_SEQ_FEATURE repeat:LRR 3 3 6.12% 0.050375089032457555 ILMN_1754489, ILMN_1717252, ILMN_1772387, 34 132 12056 8.058823529411764 1.0 1.0 67.40654846247544
  UP_SEQ_FEATURE   repeat:LRR 3
  UP_SEQ_FEATURE disulfide bond 13 26.53% 0.01293759405941519 ILMN_1741371, ILMN_1759087, ILMN_1718525, ILMN_1743329, ILMN_1748338, ILMN_1700888, ILMN_1722855, ILMN_1708779, ILMN_1767233, ILMN_1750497, ILMN_1777658, ILMN_1750234, ILMN_1780465, 34 2257 12056 2.0423779613750686 1.0 1.0 24.60526798193786
  UP_SEQ_FEATURE   disulfide bond
  SP_PIR_KEYWORDS transducer 6 12.24% 0.057294646924235346 ILMN_1759087, ILMN_1743329, ILMN_1772727, ILMN_1748338, ILMN_1714980, ILMN_1750497, 43 881 17599 2.787371644273157 1.0 0.9998747358559845 60.92937311117008
  SP_PIR_KEYWORDS transducer
  GOTERM_BP_ALL GO:0009620~response to fungus 2 4.08% 0.044754229278689765 ILMN_1708779, ILMN_1772387, 40 18 15360 42.66666666666667 1.0 1.0 58.350929107631956
  GOTERM_BP_ALL   GO:0009620~response to fungus
  GOTERM_CC_ALL GO:0005887~integral to plasma membrane 7 14.29% 0.059501566519986435 ILMN_1731745, ILMN_1741371, ILMN_1743329, ILMN_1772727, ILMN_1747683, ILMN_1780465, ILMN_1772387, 37 1246 15857 2.4076829638627393 1.0 1.0 61.39321623792138
  GOTERM_CC_ALL   GO:0005887~integral to plasma membrane
  UP_SEQ_FEATURE topological domain:Extracellular 14 28.57% 0.0022672796720831292 ILMN_1731745, ILMN_1759087, ILMN_1743329, ILMN_1747683, ILMN_1748338, ILMN_1700888, ILMN_1714980, ILMN_1772387, ILMN_1767233, ILMN_1750497, ILMN_1777658, ILMN_1772727, ILMN_1780465, ILMN_1738849, 34 2092 12056 2.3729614216623554 1.0 0.9999999994964114 4.80383877784748
  UP_SEQ_FEATURE   topological domain:Extracellular
  SP_PIR_KEYWORDS g-protein coupled receptor 6 12.24% 0.04681987018050463 ILMN_1759087, ILMN_1743329, ILMN_1772727, ILMN_1748338, ILMN_1714980, ILMN_1750497, 43 832 17599 2.95153175313059 1.0 0.9999636833469407 53.41019833781681
  SP_PIR_KEYWORDS g-protein coupled receptor
  UP_SEQ_FEATURE topological domain:Cytoplasmic 14 28.57% 0.013195267574960728 ILMN_1731745, ILMN_1759087, ILMN_1743329, ILMN_1747683, ILMN_1748338, ILMN_1700888, ILMN_1714980, ILMN_1772387, ILMN_1767233, ILMN_1750497, ILMN_1777658, ILMN_1772727, ILMN_1780465, ILMN_1738849, 34 2554 12056 1.9437099820351005 1.0 1.0 25.030994571356445
  UP_SEQ_FEATURE   topological domain:Cytoplasmic
  GOTERM_MF_ALL GO:0001871~pattern binding 3 6.12% 0.025350396961618844 ILMN_1722855, ILMN_1699735, ILMN_1772387, 36 120 16968 11.783333333333333 1.0 0.999999999979955 36.88587537377367
  GOTERM_MF_ALL   GO:0001871~pattern binding
  GOTERM_MF_ALL GO:0060089~molecular transducer activity 11 22.45% 0.029894078111325575 ILMN_1777658, ILMN_1759087, ILMN_1743329, ILMN_1772727, ILMN_1752046, ILMN_1780465, ILMN_1748338, ILMN_1714980, ILMN_1750497, ILMN_1767233, ILMN_1772387, 36 2557 16968 2.02763655325251 1.0 0.9999995240203935 41.95651509259159
  GOTERM_MF_ALL   GO:0060089~molecular transducer activity
  UP_SEQ_FEATURE repeat:LRR 2 3 6.12% 0.055934508134846746 ILMN_1754489, ILMN_1717252, ILMN_1772387, 34 140 12056 7.598319327731093 1.0 1.0 71.3038083352595
  UP_SEQ_FEATURE   repeat:LRR 2
  GOTERM_MF_ALL GO:0004930~G-protein coupled receptor activity 6 12.24% 0.044329382679716686 ILMN_1759087, ILMN_1743329, ILMN_1772727, ILMN_1748338, ILMN_1714980, ILMN_1750497, 36 953 16968 2.967471143756558 1.0 0.9999999919856024 55.63350341762754
  GOTERM_MF_ALL   GO:0004930~G-protein coupled receptor activity
  UP_SEQ_FEATURE transmembrane region 18 36.73% 0.002001285675137048 ILMN_1731745, ILMN_1741371, ILMN_1759087, ILMN_1743329, ILMN_1752813, ILMN_1747683, ILMN_1732049, ILMN_1748338, ILMN_1700888, ILMN_1714980, ILMN_1750497, ILMN_1772387, ILMN_1767233, ILMN_1777658, ILMN_1772727, ILMN_1679558, ILMN_1780465, ILMN_1738849, 34 3211 12056 1.9877260153516407 1.0 1.0 4.251872992840566
  UP_SEQ_FEATURE   transmembrane region
  GOTERM_MF_ALL GO:0001584~rhodopsin-like receptor activity 6 12.24% 0.02634256599594032 ILMN_1759087, ILMN_1743329, ILMN_1772727, ILMN_1748338, ILMN_1714980, ILMN_1750497, 36 828 16968 3.4154589371980677 1.0 0.9999999954475052 38.027567684179154
  GOTERM_MF_ALL   GO:0001584~rhodopsin-like receptor activity
  GOTERM_BP_ALL GO:0009410~response to xenobiotic stimulus 2 4.08% 0.09680892049365422 ILMN_1752813, ILMN_1708779, 40 40 15360 19.200000000000003 1.0 1.0 85.74158716169707
  GOTERM_BP_ALL   GO:0009410~response to xenobiotic stimulus
  SP_PIR_KEYWORDS glycoprotein 18 36.73% 0.004458676320668984 ILMN_1741371, ILMN_1718525, ILMN_1759087, ILMN_1743329, ILMN_1752813, ILMN_1747683, ILMN_1748338, ILMN_1700888, ILMN_1722855, ILMN_1729433, ILMN_1714980, ILMN_1772387, ILMN_1767233, ILMN_1777658, ILMN_1724424, ILMN_1772727, ILMN_1780465, ILMN_1738849, 43 3807 17599 1.9351256253779758 0.9914649707007087 0.9914649707007087 6.870422526756103
  SP_PIR_KEYWORDS glycoprotein
  SP_PIR_KEYWORDS membrane 20 40.82% 0.025822530859489445 ILMN_1731745, ILMN_1741371, ILMN_1759087, ILMN_1743329, ILMN_1752813, ILMN_1747683, ILMN_1732049, ILMN_1700888, ILMN_1748338, ILMN_1729433, ILMN_1714980, ILMN_1750497, ILMN_1772387, ILMN_1767233, ILMN_1777658, ILMN_1724424, ILMN_1772727, ILMN_1679558, ILMN_1780465, ILMN_1738849, 43 5272 17599 1.552652009739916 0.999999999999227 0.9990623331254216 34.07913985791367
  SP_PIR_KEYWORDS membrane
  UP_SEQ_FEATURE repeat:LRR 1 3 6.12% 0.055934508134846746 ILMN_1754489, ILMN_1717252, ILMN_1772387, 34 140 12056 7.598319327731093 1.0 1.0 71.3038083352595
  UP_SEQ_FEATURE   repeat:LRR 1
  SP_PIR_KEYWORDS mitogen 2 4.08% 0.08906667883999794 ILMN_1722855, ILMN_1699735, 43 39 17599 20.988670244484197 1.0 0.999996004345615 77.36990492265086
  SP_PIR_KEYWORDS mitogen
  SP_PIR_KEYWORDS receptor 9 18.37% 0.04950725285928249 ILMN_1777658, ILMN_1759087, ILMN_1743329, ILMN_1772727, ILMN_1748338, ILMN_1714980, ILMN_1750497, ILMN_1767233, ILMN_1772387, 43 1731 17599 2.1279674337995247 1.0 0.9998791523826503 55.4590073052319
  SP_PIR_KEYWORDS receptor
  GOTERM_BP_ALL GO:0006805~xenobiotic metabolic process 2 4.08% 0.08755462431164601 ILMN_1752813, ILMN_1708779, 40 36 15360 21.333333333333336 1.0 1.0 82.67139825680376
  GOTERM_BP_ALL   GO:0006805~xenobiotic metabolic process
  SP_PIR_KEYWORDS leucine-rich repeat 4 8.16% 0.023014335903258815 ILMN_1754489, ILMN_1736951, ILMN_1717252, ILMN_1772387, 43 256 17599 6.394985465116279 0.9999999999833731 0.9997447667578405 30.986331464416928
  SP_PIR_KEYWORDS leucine-rich repeat
  GOTERM_CC_ALL GO:0031226~intrinsic to plasma membrane 7 14.29% 0.06257872248122895 ILMN_1731745, ILMN_1741371, ILMN_1743329, ILMN_1772727, ILMN_1747683, ILMN_1780465, ILMN_1772387, 37 1262 15857 2.3771576647963335 1.0 0.9999999999993398 63.307078417720106
  GOTERM_CC_ALL   GO:0031226~intrinsic to plasma membrane
  GOTERM_MF_ALL GO:0004888~transmembrane receptor activity 9 18.37% 0.006275755892878886 ILMN_1777658, ILMN_1759087, ILMN_1743329, ILMN_1772727, ILMN_1748338, ILMN_1714980, ILMN_1750497, ILMN_1767233, ILMN_1772387, 36 1388 16968 3.056195965417867 0.9999999864724688 0.9999999864724688 10.670445055462363
  GOTERM_MF_ALL   GO:0004888~transmembrane receptor activity
  GOTERM_CC_ALL GO:0031224~intrinsic to membrane 18 36.73% 0.06759206385198491 ILMN_1731745, ILMN_1741371, ILMN_1759087, ILMN_1743329, ILMN_1752813, ILMN_1747683, ILMN_1732049, ILMN_1748338, ILMN_1700888, ILMN_1714980, ILMN_1750497, ILMN_1772387, ILMN_1767233, ILMN_1777658, ILMN_1724424, ILMN_1772727, ILMN_1780465, ILMN_1738849, 37 5378 15857 1.4344024202707728 1.0 0.999999746198835 66.23619399038067
  GOTERM_CC_ALL   GO:0031224~intrinsic to membrane
  PIR_SUPERFAMILY PIRSF036848:conserved protein with F-box/LRR-repeat, Skp2 type 2 4.08% 0.02445880409797784 ILMN_1754489, ILMN_1717252, 20 9 6919 76.87777777777778 1.0 1.0 36.09156185764799
  PIR_SUPERFAMILY PIRSF036848:conserved protein with F-box/LRR-repeat, Skp2 type
  UP_SEQ_FEATURE glycosylation site:N-linked (GlcNAc...) 15 30.61% 0.02576746177407038 ILMN_1741371, ILMN_1718525, ILMN_1759087, ILMN_1743329, ILMN_1752813, ILMN_1747683, ILMN_1748338, ILMN_1700888, ILMN_1714980, ILMN_1772387, ILMN_1767233, ILMN_1777658, ILMN_1772727, ILMN_1780465, ILMN_1738849, 34 3085 12056 1.7240919058060824 1.0 1.0 43.23178380844887
  UP_SEQ_FEATURE   glycosylation site:N-linked (GlcNAc...)
  SP_PIR_KEYWORDS transmembrane 19 38.78% 0.009679126085189019 ILMN_1731745, ILMN_1741371, ILMN_1759087, ILMN_1743329, ILMN_1752813, ILMN_1747683, ILMN_1732049, ILMN_1700888, ILMN_1748338, ILMN_1714980, ILMN_1750497, ILMN_1772387, ILMN_1767233, ILMN_1777658, ILMN_1724424, ILMN_1772727, ILMN_1679558, ILMN_1780465, ILMN_1738849, 43 4452 17599 1.7466986355753358 0.9999685844429379 0.9943950417430579 14.351966656994787
  SP_PIR_KEYWORDS transmembrane
  GOTERM_CC_ALL GO:0016021~integral to membrane 18 36.73% 0.06535743736236507 ILMN_1731745, ILMN_1741371, ILMN_1759087, ILMN_1743329, ILMN_1752813, ILMN_1747683, ILMN_1732049, ILMN_1748338, ILMN_1700888, ILMN_1714980, ILMN_1750497, ILMN_1772387, ILMN_1767233, ILMN_1777658, ILMN_1724424, ILMN_1772727, ILMN_1780465, ILMN_1738849, 37 5357 15857 1.4400254277050994 1.0 0.9999999967879639 64.95870291365749
  GOTERM_CC_ALL   GO:0016021~integral to membrane
  GOTERM_MF_ALL GO:0004872~receptor activity 10 20.41% 0.024445864559518166 ILMN_1777658, ILMN_1759087, ILMN_1743329, ILMN_1772727, ILMN_1780465, ILMN_1748338, ILMN_1714980, ILMN_1750497, ILMN_1767233, ILMN_1772387, 36 2113 16968 2.2306357469632436 1.0 0.9999999999999997 35.82774717503101
  GOTERM_MF_ALL   GO:0004872~receptor activity
  INTERPRO IPR000276:Rhodopsin-like GPCR superfamily 6 12.24% 0.02736075111434335 ILMN_1759087, ILMN_1743329, ILMN_1772727, ILMN_1748338, ILMN_1714980, ILMN_1750497, 42 747 17845 3.4126984126984126 1.0 1.0 41.56899259261204
  INTERPRO   IPR000276:Rhodopsin-like GPCR superfamily
  GOTERM_MF_ALL GO:0004871~signal transducer activity 11 22.45% 0.029894078111325575 ILMN_1777658, ILMN_1759087, ILMN_1743329, ILMN_1772727, ILMN_1752046, ILMN_1780465, ILMN_1748338, ILMN_1714980, ILMN_1750497, ILMN_1767233, ILMN_1772387, 36 2557 16968 2.02763655325251 1.0 0.9999995240203935 41.95651509259159
  GOTERM_MF_ALL   GO:0004871~signal transducer activity
* '''FUNCTIONAL CATEGORIES''' (Important info here...)

Revision as of 23:43, 13 May 2009

iPS Cancer?

  • Obtained Illumina Array data from Dr. Zhang
  • Used SAM and DAVID to try and identify GO Terms in differentially expressed genes.
  • Say we want a desired FDR of 15% or lower; since we are just doing preliminary.
  • SAM's multiclass feature is not useful here; it will call everything that is fibroblast-only "significant," leading to numbers that are far too large.

Very Lenient

  • Very lenient analysis results in a large amount of GO Terms and GO Clusters.
  • Delta of 2.3 was used for IPS_HESC
  • Delta of 0.1 (very low, since figured a lot of genes would need to be called as "not similar")
  • Will upload DAVID results to Wiki.
  • Lots of very interesting GO terms and GO clusters
  • However, inspection of several reveals that these values may be too lenient. Lots of things are called as significant that are not very.

Very Stringent

  • Limited ESC_IPS differences to 475, limited GO differences to 250.
  • In this case, only 3 or 4 clusters were obtained at all (only 23 diff. expressed genes)
  • Most of them have very low scores...probably too stringent here

New Method

  • It seems SAM has issues finding differences between fibroblasts and IPS that are meaningful
  • Because so many genes are differentially expressed already, very hard to choose a proper delta value.
    • FDR is predicted to be very high.
  • Instead, will find differentially expressed genes between IPS and HESC first.
    • Only look at these in Fibroblasts, then run SAM!
  • Should help find any genes that do not match normal Fibroblasts or hESC in iPS cells.
  • Should help find some new behavior.

Procedure

  • First, run SAM on Illumina sequencing data for just iPS and hESC.
  • Extract differentially expressed genes such that the FDR is 0.05
    • Turned out to be a delta of 1.7 with 4365 differentially expressed genes.
  • Extracted data for just this gene subset from Illumina data, and only for FIBROBLASTS and IPS.
    • Saved file in NewMethod folder as csv
  • Imported into R, ran SAM again.
    • Interesting results.
    • Pulled out at Delta=4 in order to obtain FDR of 0.2...FDR never went below 0.04 even after just one gene was being called significant. Delta of 4 gave around 50 genes to work with.
    • In one way, this is decent news; means that iPS cells do not stray too far from fibroblasts...
    • However, several of the GO groups are interesting.
  • Differentially expressed genes (from SAM):
ILLUMINA_ID  	Gene Name  	Related Genes  	Species
ILMN_1731745 	ninjurin 2 	RG 	Homo sapiens
ILMN_1759087 	olfactory receptor, family 10, subfamily v, member 1 	RG 	Homo sapiens
ILMN_1662021 	hypothetical protein flj20403 similar to zinc finger protein 326 	RG 	Homo sapiens
ILMN_1702568 	chromosome 9 open reading frame 28 	RG 	Homo sapiens
ILMN_1722855 	vascular endothelial growth factor b 	RG 	Homo sapiens
ILMN_1714980 	mas-related gpr, member d 	RG 	Homo sapiens
ILMN_1772387 	toll-like receptor 2 	RG 	Homo sapiens
ILMN_1767233 	ectodysplasin a2 receptor 	RG 	Homo sapiens
ILMN_1795336 	phosphotriesterase related 	RG 	Homo sapiens
ILMN_1772727 	g protein-coupled receptor 75 	RG 	Homo sapiens
ILMN_1679558 	hypothetical protein flj20393 	RG 	Homo sapiens
ILMN_1780465 	c-type lectin domain family 5, member a 	RG 	Homo sapiens
ILMN_1743329 	retinal pigment epithelium-derived rhodopsin homolog 	RG 	Homo sapiens
ILMN_1752813 	udp glucuronosyltransferase 1 family, polypeptide a6 	RG 	Homo sapiens
ILMN_1754553 	mediator of rna polymerase ii transcription, subunit 19 homolog (yeast) 	RG 	Homo sapiens
ILMN_1700766 	flj45850 protein 	RG 	Homo sapiens 
ILMN_1736951 	leucine-rich repeats and iq motif containing 2 	RG 	Homo sapiens
ILMN_1747683 	aquaporin 4 	RG 	Homo sapiens
ILMN_1717579 	chromosome 17 open reading frame 64 	RG 	Homo sapiens
ILMN_1708779 	granulysin 	RG 	Homo sapiens
ILMN_1764201 	microtubule-associated protein 2 	RG 	Homo sapiens
ILMN_1724424 	proline-rich transmembrane protein 2 	RG 	Homo sapiens
ILMN_1750234 	protease, serine, 2 (trypsin 2) 	RG 	Homo sapiens
ILMN_1726928 	transcription elongation factor a (sii), 3 	RG 	Homo sapiens
ILMN_1752046 	lymphocyte adaptor protein 	RG 	Homo sapiens
ILMN_1717252 	f-box and leucine-rich repeat protein 21 	RG 	Homo sapiens
ILMN_1680932 	hypothetical protein flj12492 	RG 	Homo sapiens
ILMN_1709953 	downstream neighbor of son 	RG 	Homo sapiens
ILMN_1748338 	g protein-coupled receptor 85 	RG 	Homo sapiens
ILMN_1700888 	ectonucleotide pyrophosphatase/phosphodiesterase 1 	RG 	Homo sapiens
ILMN_1729433 	lipase, member h 	RG 	Homo sapiens
ILMN_1750497 	g protein-coupled receptor 109a 	RG 	Homo sapiens
ILMN_1757521 	creatine kinase, muscle 	RG 	Homo sapiens
ILMN_1706266 	ring finger protein 157 	RG 	Homo sapiens
ILMN_1729203 	protein disulfide isomerase-like protein of the testis 	RG 	Homo sapiens
ILMN_1738849 	solute carrier family 9 (sodium/hydrogen exchanger), member 2 	RG 	Homo sapiens
ILMN_1706590 	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, drosophila); translocated to, 1 	RG 	Homo sapiens
ILMN_1741371 	transmembrane protein 8 (five membrane-spanning domains) 	RG 	Homo sapiens
ILMN_1769538 	flj36268 protein 	RG 	Homo sapiens
ILMN_1718525 	inter-alpha (globulin) inhibitor h4 (plasma kallikrein-sensitive glycoprotein) 	RG 	Homo sapiens
ILMN_1732049 	dolichyl-phosphate mannosyltransferase polypeptide 2, regulatory subunit 	RG 	Homo sapiens
ILMN_1798957 	chromosome 12 open reading frame 47 	RG 	Homo sapiens
ILMN_1699735 	fibroblast growth factor 1 (acidic) 	RG 	Homo sapiens
ILMN_1777658 	scavenger receptor class f, member 1 	RG 	Homo sapiens
ILMN_1780172 	chromosome 20 open reading frame 195 	RG 	Homo sapiens
ILMN_1722502 	chaperonin containing tcp1, subunit 6a (zeta 1) 	RG 	Homo sapiens
ILMN_1748884 	transducer of erbb2, 2 	RG 	Homo sapiens
ILMN_1754489 	f-box and leucine-rich repeat protein 20 	RG 	Homo sapiens
ILMN_1753648 	tripartite motif-containing 51 	RG 	Homo sapiens
  • GO Terms associated with this set:
Category	  Term
UP_SEQ_FEATURE	  repeat:LRR 3
UP_SEQ_FEATURE	  disulfide bond
SP_PIR_KEYWORDS  transducer
GOTERM_BP_ALL	  GO:0009620~response to fungus
GOTERM_CC_ALL	  GO:0005887~integral to plasma membrane
UP_SEQ_FEATURE	  topological domain:Extracellular
SP_PIR_KEYWORDS  g-protein coupled receptor
UP_SEQ_FEATURE	  topological domain:Cytoplasmic
GOTERM_MF_ALL	  GO:0001871~pattern binding
GOTERM_MF_ALL	  GO:0060089~molecular transducer activity
UP_SEQ_FEATURE	  repeat:LRR 2
GOTERM_MF_ALL	  GO:0004930~G-protein coupled receptor activity
UP_SEQ_FEATURE	  transmembrane region
GOTERM_MF_ALL	  GO:0001584~rhodopsin-like receptor activity
GOTERM_BP_ALL	  GO:0009410~response to xenobiotic stimulus
SP_PIR_KEYWORDS  glycoprotein
SP_PIR_KEYWORDS  membrane
UP_SEQ_FEATURE   repeat:LRR 1
SP_PIR_KEYWORDS  mitogen
SP_PIR_KEYWORDS  receptor
GOTERM_BP_ALL	  GO:0006805~xenobiotic metabolic process
SP_PIR_KEYWORDS  leucine-rich repeat
GOTERM_CC_ALL	  GO:0031226~intrinsic to plasma membrane
GOTERM_MF_ALL	  GO:0004888~transmembrane receptor activity
GOTERM_CC_ALL	  GO:0031224~intrinsic to membrane
PIR_SUPERFAMILY  PIRSF036848:conserved protein with F-box/LRR-repeat, Skp2 type
UP_SEQ_FEATURE   glycosylation site:N-linked (GlcNAc...)
SP_PIR_KEYWORDS  transmembrane
GOTERM_CC_ALL	  GO:0016021~integral to membrane
GOTERM_MF_ALL	  GO:0004872~receptor activity
INTERPRO	  IPR000276:Rhodopsin-like GPCR superfamily
GOTERM_MF_ALL	  GO:0004871~signal transducer activity
  • FUNCTIONAL CATEGORIES (Important info here...)