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