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	Hugo	description	Value Type	Network Comparison Type	Interaction Map	Filtered	red	green	network_comparison

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Showing element 951 to 1000 of 3228 in total

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

Rank	Hugo	description	red	green	network_comparison
951	TRIO	triple functional domain protein (ptprf interacting protein). [swissprot;acc:o75962]	217.253	209.827	1.03539
952	TOM1L2	target of myb1-like 2; target of myb1 (chicken) homolog-like 2. [refseq;acc:nm_144678]	217.252	209.83	1.03537
953	EXOSC10	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	205.466	1.03512
954	GSTZ1	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	276.773	1.03487
955	MRPL27	mitochondrial 60s ribosomal protein l27 (l27mt) (hspc250). [swissprot;acc:q9p0m9]	231.163	239.205	1.03479
956	SORBS3	vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504]	211.812	204.732	1.03458
957	ARAF	a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398]	129.913	134.399	1.03453
958	RAF1	raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049]	129.921	134.406	1.03452
959	no value	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	229.677	1.03431
960	ZRF1	zuotin related factor-1 (m-phase phosphoprotein 11). [swissprot;acc:q99543]
961	PPP2R5E	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	134.527	1.0343
962	CCNG2	cyclin g2. [swissprot;acc:q16589]
963	CCNG1	cyclin g1 (cyclin g). [swissprot;acc:p51959]
964	PPP2R5A	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	PARD6G	partitioning defective-6 homolog gamma (par-6 gamma) (par6d). [swissprot;acc:q9byg4]	211.987	204.964	1.03426
966	TUB	tubby protein homolog. [swissprot;acc:p50607]
967	PRKCI	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	numb protein homolog (h-numb) (protein s171). [swissprot;acc:p49757]
969	TBC1D5	tbc1 domain family member 5. [swissprot;acc:q92609]
970	TULP1	tubby related protein 1 (tubby-like protein 1). [swissprot;acc:o00294]
971	VPS29	vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [swissprot;acc:q9ubq0]
972	NUMBL	numb-like protein (numb-r). [swissprot;acc:q9y6r0]
973	TULP3	tubby related protein 3 (tubby-like protein 3). [swissprot;acc:o75386]
974	VPS35	vacuolar protein sorting 35 (vesicle protein sorting 35) (hvps35) (maternal-embryonic 3). [swissprot;acc:q96qk1]
975	PRKCZ	protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [swissprot;acc:q05513]
976	WDR36	t-cell activation wd repeat protein. [refseq;acc:nm_139281]	243.34	235.322	1.03407
977	PFDN5	prefoldin subunit 5 (c-myc binding protein mm-1) (myc modulator 1). [swissprot;acc:q99471]	228.953	221.421	1.03402
978	no value	prefoldin subunit 6 (protein ke2). [swissprot;acc:o15212]
979	BLOC1S1	gcn5-like protein 1 (rt14 protein). [swissprot;acc:p78537]	202.027	195.386	1.03399
980	BRAF	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	134.713	1.03396
981	EXOC3	exocyst complex component sec6. [swissprot;acc:o60645]	207.186	200.398	1.03387
982	CIRH1A	cirhin; testis expressed gene 292; cirrhosis, autosomal recessive 1a. [refseq;acc:nm_032830]	243.312	235.351	1.03383
983	RSL1D1	pbk1 protein. [sptrembl;acc:o76021]		235.353	1.03382
984	PAPOLA	poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003]	116.71	120.654	1.03379
985	PDCD5	programmed cell death protein 5 (tfar19 protein) (tf-1 cell apoptosis related gene-19 protein). [swissprot;acc:o14737]	233.402	225.782	1.03375
986	EXOC2	exocyst complex component sec5. [swissprot;acc:q96kp1]	116.771	120.707	1.03371
987	HTRA2	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	211.338	1.03369
988	HTRA4	probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105]	218.461	211.343	1.03368
989	HTRA3	probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110]	218.462	211.345	1.03367
990	DDX52	atp-dependent rna helicase rok1; atp-dependent rna helicase. [refseq;acc:nm_007010]	243.297	235.373
991	DPM1	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	196.76	1.03365
992	HTRA1	serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743]	218.468	211.357	1.03364
993	PNN	pinin, desmosome associated protein; pinin. [refseq;acc:nm_002687]	211.071	204.205	1.03362
994	PAPOLG	poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3]	116.845	120.772	1.03361
995	MAD2L2	mitotic spindle assembly checkpoint protein mad2b (mad2-like 2) (hrev7). [swissprot;acc:q9ui95]	219.656	212.547	1.03345
996	no value	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]
997	NUP88	nuclear pore complex protein nup88 (nucleoporin nup88) (88 kda nuclear pore complex protein). [swissprot;acc:q99567]
998	DYNC1I2	dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [swissprot;acc:q13409]	225.557	218.271	1.03338
999	VCL	vinculin (metavinculin). [swissprot;acc:p18206]	215.92	208.95	1.03336
1000	no value	sprouty homolog 4 (spry-4). [swissprot;acc:q9c004]	225.167	217.922	1.03325

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
- Hugo is the HGNC identifier if it exists
- 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.