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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Rank Gene description Network Comparison Type Value Type Interaction Map Filtered green red network_comparison
Results: HTML CSV LaTeX Showing element 1950 to 1999 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
green
red
network_comparison
975 protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [swissprot;acc:q05513] Divided 204.964 211.987 1.03426
976 retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] Subtracted 125.389 132.413 7.024
t-cell activation wd repeat protein. [refseq;acc:nm_139281] Divided 235.322 243.34 1.03407
977 partitioning defective-6 homolog gamma (par-6 gamma) (par6d). [swissprot;acc:q9byg4] Subtracted 204.964 211.987 7.023
prefoldin subunit 5 (c-myc binding protein mm-1) (myc modulator 1). [swissprot;acc:q99471] Divided 221.421 228.953 1.03402
978 prefoldin subunit 6 (protein ke2). [swissprot;acc:o15212]
tubby protein homolog. [swissprot;acc:p50607] Subtracted 204.964 211.987 7.023
979 gcn5-like protein 1 (rt14 protein). [swissprot;acc:p78537] Divided 195.386 202.027 1.03399
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 204.964 211.987 7.023
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 134.713 130.289 1.03396
numb protein homolog (h-numb) (protein s171). [swissprot;acc:p49757] Subtracted 204.964 211.987 7.023
981 exocyst complex component sec6. [swissprot;acc:o60645] Divided 200.398 207.186 1.03387
tbc1 domain family member 5. [swissprot;acc:q92609] Subtracted 204.964 211.987 7.023
982 cirhin; testis expressed gene 292; cirrhosis, autosomal recessive 1a. [refseq;acc:nm_032830] Divided 235.351 243.312 1.03383
tubby related protein 1 (tubby-like protein 1). [swissprot;acc:o00294] Subtracted 204.964 211.987 7.023
983 pbk1 protein. [sptrembl;acc:o76021] Divided 235.353 243.312 1.03382
vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [swissprot;acc:q9ubq0] Subtracted 204.964 211.987 7.023
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 120.654 116.71 1.03379
985 programmed cell death protein 5 (tfar19 protein) (tf-1 cell apoptosis related gene-19 protein). [swissprot;acc:o14737] 225.782 233.402 1.03375
tubby related protein 3 (tubby-like protein 3). [swissprot;acc:o75386] Subtracted 204.964 211.987 7.023
986 exocyst complex component sec5. [swissprot;acc:q96kp1] Divided 120.707 116.771 1.03371
vacuolar protein sorting 35 (vesicle protein sorting 35) (hvps35) (maternal-embryonic 3). [swissprot;acc:q96qk1] Subtracted 204.964 211.987 7.023
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 211.338 218.459 1.03369
988 probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105] 211.343 218.461 1.03368
similar to zinc finger protein 277. [sptrembl;acc:q8wwa6] Subtracted 243.679 236.679 7
989 probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110] Divided 211.345 218.462 1.03367
zinc finger protein 277. [swissprot;acc:q9nrm2] Subtracted 243.679 236.679 7
990 atp-dependent rna helicase rok1; atp-dependent rna helicase. [refseq;acc:nm_007010] Divided 235.373 243.297 1.03367
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 228.68 221.682 6.998
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 196.76 203.381 1.03365
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 205.466 198.494 6.972
992 serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743] Divided 211.357 218.468 1.03364
vinculin (metavinculin). [swissprot;acc:p18206] Subtracted 208.95 215.92 6.97
993 hepatocyte nuclear factor 4-gamma (hnf-4-gamma). [swissprot;acc:q14541] 258.829 251.863 6.966
pinin, desmosome associated protein; pinin. [refseq;acc:nm_002687] Divided 204.205 211.071 1.03362
994 growth arrest and dna-damage-inducible protein gadd45 gamma (cytokine responsive protein cr6). [swissprot;acc:o95257] Subtracted 258.829 251.863 6.966
poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] Divided 120.772 116.845 1.03361
995 growth arrest and dna-damage-inducible protein gadd45 alpha (dna- damage inducible transcript 1) (ddit1). [swissprot;acc:p24522] Subtracted 258.829 251.863 6.966
mitotic spindle assembly checkpoint protein mad2b (mad2-like 2) (hrev7). [swissprot;acc:q9ui95] Divided 212.547 219.656 1.03345
996 hepatocyte nuclear factor 4-alpha (hnf-4-alpha) (transcription factor hnf-4) (transcription factor 14). [swissprot;acc:p41235] Subtracted 258.829 251.863 6.966
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] Divided 212.547 219.656 1.03345
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 258.829 251.863 6.966
nuclear pore complex protein nup88 (nucleoporin nup88) (88 kda nuclear pore complex protein). [swissprot;acc:q99567] Divided 212.547 219.656 1.03345
998 dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [swissprot;acc:q13409] 218.271 225.557 1.03338
tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677] Subtracted 214.409 221.302 6.893
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] 276.493 269.608 6.885
vinculin (metavinculin). [swissprot;acc:p18206] Divided 208.95 215.92 1.03336
1000 peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [swissprot;acc:q9ukg9] Subtracted 210.648 217.523 6.875

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/