MK5 Microarray Data

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	red	network_comparison	green

Results: HTML CSV LaTeX

Showing element 951 to 1000 of 3228 in total

Network Comparison Type  : Divided
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1

Rank	description	red	network_comparison	green
951	triple functional domain protein (ptprf interacting protein). [swissprot;acc:o75962]	217.253	1.03539	209.827
952	target of myb1-like 2; target of myb1 (chicken) homolog-like 2. [refseq;acc:nm_144678]	217.252	1.03537	209.83
953	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]	198.494	1.03512	205.466
954	maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [swissprot;acc:o43708]	267.447	1.03487	276.773
955	mitochondrial 60s ribosomal protein l27 (l27mt) (hspc250). [swissprot;acc:q9p0m9]	231.163	1.03479	239.205
956	vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504]	211.812	1.03458	204.732
957	a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398]	129.913	1.03453	134.399
958	raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049]	129.921	1.03452	134.406
959	guanine nucleotide-binding protein beta subunit-like protein 12.3 (p205) (receptor of activated protein kinase c 1) (rack1) (receptor for activated c kinase). [swissprot;acc:p25388]	237.558	1.03431	229.677
960	zuotin related factor-1 (m-phase phosphoprotein 11). [swissprot;acc:q99543]
961	serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, epsilon isoform (pp2a, b subunit, b' epsilon isoform) (pp2a, b subunit, b56 epsilon isoform) (pp2a, b subunit, pr61 epsilon isoform) (pp2a, b subunit, r5 epsilon isoform). [swissprot;acc:q16537]	130.066	1.0343	134.527
962	cyclin g2. [swissprot;acc:q16589]
963	cyclin g1 (cyclin g). [swissprot;acc:p51959]
964	serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, alpha isoform (pp2a, b subunit, b' alpha isoform) (pp2a, b subunit, b56 alpha isoform) (pp2a, b subunit, pr61 alpha isoform) (pp2a, b subunit, r5 alpha isoform). [swissprot;acc:q15172]
965	partitioning defective-6 homolog gamma (par-6 gamma) (par6d). [swissprot;acc:q9byg4]	211.987	1.03426	204.964
966	tubby protein homolog. [swissprot;acc:p50607]
967	protein kinase c, iota type (ec 2.7.1.37) (npkc-iota) (atypical protein kinase c-lamda/iota) (apkc-lambda/iota). [swissprot;acc:p41743]
968	numb protein homolog (h-numb) (protein s171). [swissprot;acc:p49757]
969	tbc1 domain family member 5. [swissprot;acc:q92609]
970	tubby related protein 1 (tubby-like protein 1). [swissprot;acc:o00294]
971	vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [swissprot;acc:q9ubq0]
972	numb-like protein (numb-r). [swissprot;acc:q9y6r0]
973	tubby related protein 3 (tubby-like protein 3). [swissprot;acc:o75386]
974	vacuolar protein sorting 35 (vesicle protein sorting 35) (hvps35) (maternal-embryonic 3). [swissprot;acc:q96qk1]
975	protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [swissprot;acc:q05513]
976	t-cell activation wd repeat protein. [refseq;acc:nm_139281]	243.34	1.03407	235.322
977	prefoldin subunit 5 (c-myc binding protein mm-1) (myc modulator 1). [swissprot;acc:q99471]	228.953	1.03402	221.421
978	prefoldin subunit 6 (protein ke2). [swissprot;acc:o15212]
979	gcn5-like protein 1 (rt14 protein). [swissprot;acc:p78537]	202.027	1.03399	195.386
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]	130.289	1.03396	134.713
981	exocyst complex component sec6. [swissprot;acc:o60645]	207.186	1.03387	200.398
982	cirhin; testis expressed gene 292; cirrhosis, autosomal recessive 1a. [refseq;acc:nm_032830]	243.312	1.03383	235.351
983	pbk1 protein. [sptrembl;acc:o76021]		1.03382	235.353
984	poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003]	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
986	exocyst complex component sec5. [swissprot;acc:q96kp1]	116.771	1.03371	120.707
987	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]	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
989	probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110]	218.462	1.03367	211.345
990	atp-dependent rna helicase rok1; atp-dependent rna helicase. [refseq;acc:nm_007010]	243.297		235.373
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]	203.381	1.03365	196.76
992	serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743]	218.468	1.03364	211.357
993	pinin, desmosome associated protein; pinin. [refseq;acc:nm_002687]	211.071	1.03362	204.205
994	poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3]	116.845	1.03361	120.772
995	mitotic spindle assembly checkpoint protein mad2b (mad2-like 2) (hrev7). [swissprot;acc:q9ui95]	219.656	1.03345	212.547
996	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]
997	nuclear pore complex protein nup88 (nucleoporin nup88) (88 kda nuclear pore complex protein). [swissprot;acc:q99567]
998	dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [swissprot;acc:q13409]	225.557	1.03338	218.271
999	vinculin (metavinculin). [swissprot;acc:p18206]	215.92	1.03336	208.95
1000	sprouty homolog 4 (spry-4). [swissprot;acc:q9c004]	225.167	1.03325	217.922

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.