Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


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Gene Rank description Value Type Network Comparison Type Interaction Map Filtered red network_comparison green
Results: HTML CSV LaTeX Showing element 1958 to 2007 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
network_comparison
green
979 protein kinase c, iota type (ec 2.7.1.37) (npkc-iota) (atypical protein kinase c-lamda/iota) (apkc-lambda/iota). [swissprot;acc:p41743] Subtracted 211.987 7.023 204.964
980 b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056] Divided 130.289 1.03396 134.713
numb protein homolog (h-numb) (protein s171). [swissprot;acc:p49757] Subtracted 211.987 7.023 204.964
981 exocyst complex component sec6. [swissprot;acc:o60645] Divided 207.186 1.03387 200.398
tbc1 domain family member 5. [swissprot;acc:q92609] Subtracted 211.987 7.023 204.964
982 cirhin; testis expressed gene 292; cirrhosis, autosomal recessive 1a. [refseq;acc:nm_032830] Divided 243.312 1.03383 235.351
tubby related protein 1 (tubby-like protein 1). [swissprot;acc:o00294] Subtracted 211.987 7.023 204.964
983 pbk1 protein. [sptrembl;acc:o76021] Divided 243.312 1.03382 235.353
vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [swissprot;acc:q9ubq0] Subtracted 211.987 7.023 204.964
984 numb-like protein (numb-r). [swissprot;acc:q9y6r0]
poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] Divided 116.71 1.03379 120.654
985 programmed cell death protein 5 (tfar19 protein) (tf-1 cell apoptosis related gene-19 protein). [swissprot;acc:o14737] 233.402 1.03375 225.782
tubby related protein 3 (tubby-like protein 3). [swissprot;acc:o75386] Subtracted 211.987 7.023 204.964
986 exocyst complex component sec5. [swissprot;acc:q96kp1] Divided 116.771 1.03371 120.707
vacuolar protein sorting 35 (vesicle protein sorting 35) (hvps35) (maternal-embryonic 3). [swissprot;acc:q96qk1] Subtracted 211.987 7.023 204.964
987 protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [swissprot;acc:q05513]
serine protease htra2, mitochondrial precursor (ec 3.4.21.-) (high temperature requirement protein a2) (htra2) (omi stress-regulated endoprotease) (serine proteinase omi). [swissprot;acc:o43464] Divided 218.459 1.03369 211.338
988 probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105] 218.461 1.03368 211.343
similar to zinc finger protein 277. [sptrembl;acc:q8wwa6] Subtracted 236.679 7 243.679
989 probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110] Divided 218.462 1.03367 211.345
zinc finger protein 277. [swissprot;acc:q9nrm2] Subtracted 236.679 7 243.679
990 atp-dependent rna helicase rok1; atp-dependent rna helicase. [refseq;acc:nm_007010] Divided 243.297 1.03367 235.373
atrophin-1 interacting protein 1; activin receptor interacting protein 1; likely ortholog of mouse activin receptor interacting protein 1; atrophin-1 interacting protein a; membrane associated guanylate kinase 2; activin receptor interacting p. [refseq;acc:nm_012301] Subtracted 221.682 6.998 228.68
991 dolichol-phosphate mannosyltransferase (ec 2.4.1.83) (dolichol- phosphate mannose synthase) (dolichyl-phosphate beta-d- mannosyltransferase) (mannose-p-dolichol synthase) (mpd synthase) (dpm synthase). [swissprot;acc:o60762] Divided 203.381 1.03365 196.76
polymyositis/scleroderma autoantigen 2 (autoantigen pm/scl 2) (polymyositis/scleroderma autoantigen 100 kda) (pm/scl-100) (p100 polymyositis-scleroderma overlap syndrome associated autoantigen). [swissprot;acc:q01780] Subtracted 198.494 6.972 205.466
992 serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743] Divided 218.468 1.03364 211.357
vinculin (metavinculin). [swissprot;acc:p18206] Subtracted 215.92 6.97 208.95
993 hepatocyte nuclear factor 4-gamma (hnf-4-gamma). [swissprot;acc:q14541] 251.863 6.966 258.829
pinin, desmosome associated protein; pinin. [refseq;acc:nm_002687] Divided 211.071 1.03362 204.205
994 growth arrest and dna-damage-inducible protein gadd45 gamma (cytokine responsive protein cr6). [swissprot;acc:o95257] Subtracted 251.863 6.966 258.829
poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] Divided 116.845 1.03361 120.772
995 growth arrest and dna-damage-inducible protein gadd45 alpha (dna- damage inducible transcript 1) (ddit1). [swissprot;acc:p24522] Subtracted 251.863 6.966 258.829
mitotic spindle assembly checkpoint protein mad2b (mad2-like 2) (hrev7). [swissprot;acc:q9ui95] Divided 219.656 1.03345 212.547
996 hepatocyte nuclear factor 4-alpha (hnf-4-alpha) (transcription factor hnf-4) (transcription factor 14). [swissprot;acc:p41235] Subtracted 251.863 6.966 258.829
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] Divided 219.656 1.03345 212.547
997 growth arrest and dna-damage-inducible protein gadd45 beta (negative growth-regulatory protein myd118) (myeloid differentiation primary response protein myd118). [swissprot;acc:o75293] Subtracted 251.863 6.966 258.829
nuclear pore complex protein nup88 (nucleoporin nup88) (88 kda nuclear pore complex protein). [swissprot;acc:q99567] Divided 219.656 1.03345 212.547
998 dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [swissprot;acc:q13409] 225.557 1.03338 218.271
tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677] Subtracted 221.302 6.893 214.409
999 skeletal muscle lim-protein 3 (slim 3) (lim-domain protein dral) (four and a half lim domains protein 2) (fhl-2). [swissprot;acc:q14192] 269.608 6.885 276.493
vinculin (metavinculin). [swissprot;acc:p18206] Divided 215.92 1.03336 208.95
1000 peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [swissprot;acc:q9ukg9] Subtracted 217.523 6.875 210.648
sprouty homolog 4 (spry-4). [swissprot;acc:q9c004] Divided 225.167 1.03325 217.922
1001 dopachrome tautomerase precursor (ec 5.3.3.12) (dt) (dct) (dopachrome delta-isomerase) (tyrosinase-related protein 2) (trp-2) (trp2). [swissprot;acc:p40126] Subtracted 221.28 6.871 214.409
sprouty homolog 3 (spry-3). [swissprot;acc:o43610] Divided 225.167 1.03325 217.922
1002 5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643] Subtracted 221.278 6.869 214.409
sprouty homolog 1 (spry-1) (fragment). [swissprot;acc:o43609] Divided 225.167 1.03325 217.922
1003 pinin, desmosome associated protein; pinin. [refseq;acc:nm_002687] Subtracted 211.071 6.866 204.205
sprouty homolog 2 (spry-2). [swissprot;acc:o43597] Divided 225.167 1.03325 217.922
1004 sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633] 238.725 1.03318 231.059

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.
- http://analysis.yellowcouch.org/