Athurva Gore/LabNotes/ExomeReseq/2009-5-13

From ZhangLabWiki
Revision as of 23:43, 13 May 2009 by >Ajgore
Jump to navigation Jump to search

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...)