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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Gene	Filtered	Network Comparison Type	Value Type	network_comparison	Interaction Map	Rank	red	description	green

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Showing element 1001 to 1050 of 77072 in total

Filtered  : 0
Network Comparison Type  : Divided
Value Type  : Measured

network_comparison	Interaction Map	Rank	red	description	green
1.23065	Low confidence	167	4088.01	spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [swissprot;acc:q9nrc6]	3321.82
1.23201		166	1208.65	elongation of very long chain fatty acids protein 2. [swissprot;acc:q9nxb9]	1489.07
1.23523	High confidence	178	498.07	dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4v7]	615.233
	Low confidence	165
1.23683	High confidence	177	4131.06	acrc protein; putative nuclear protein. [refseq;acc:nm_052957]	3340.03
1.2405	Low confidence	164	3888.6	myotubularin related protein 8. [refseq;acc:nm_017677]	4823.8
1.24111	High confidence	176	3023.85	small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072]	2436.4
1.24677	Low confidence	163	1113.87	voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02]	1388.74
1.24887	High confidence	175	1382.5	cylindromatosis (turban tumor syndrome); cylindromatosis 1, turban tumor syndrome. [refseq;acc:nm_015247]	1107
	Low confidence	162
1.25		161	76	protein c20orf142 precursor. [swissprot;acc:q8n6m3]	95
1.25401		160	642.672	testican-3 precursor. [swissprot;acc:q9bq16]	805.916
1.25423	High confidence	174	488.43	dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2]	612.604
	Low confidence	159
1.25474		158	752.839	rho guanine nucleotide exchange factor (gef) 12; leukemia-associated rho guanine nucleotide exchange factor. [refseq;acc:nm_015313]	944.615
1.25567		157	1117.36	brca1 associated protein. [refseq;acc:nm_006768]	1403.03
1.25656	High confidence	173	3265.25	cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]	4102.97
1.25772		170	112.666	williams-beuren syndrome critical region protein 20 copy b. [refseq;acc:nm_145645]	141.702
		171		williams beuren syndrome critical region 20a isoform 2; nol1/nop2/sun gene family member; williams-beuren syndrome critical region protein 20 copy a; williams beuren syndrome chromosome region 20. [refseq;acc:nm_018044]
		172		williams beuren syndrome chromosome region 20c isoform 1. [refseq;acc:nm_032158]
1.25773		169	244	gaba-a receptor-associated protein. [sptrembl;acc:q9by60]	194
1.2585		168	334.012	transcription factor mafg (v-maf musculoaponeurotic fibrosarcoma oncogene homolog g) (hmaf). [swissprot;acc:o15525]	420.355
1.25858	Low confidence	156	1683.2	protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236]	2118.44
1.26047	High confidence	167	331.61	transcription factor mafk (erythroid transcription factor nf-e2 p18 subunit). [swissprot;acc:o60675]	417.983
1.2611		166	5629.62	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	7099.51
1.26251		165	1002.2	mto1 protein homolog (cgi-02). [swissprot;acc:q9y2z2]	793.818
1.26273	Low confidence	155	4230.36	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	5341.81
1.26383	High confidence	164	1711.55	aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181]	1354.26
1.26419	Low confidence	153	2232	candidate tumor suppressor protein. [refseq;acc:nm_020381]	2821.67
		154		supervillin isoform 1; membrane-associated f-actin binding protein p205; archvillin. [refseq;acc:nm_003174]
1.26442	High confidence	163	7830.62	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]	6193.07
1.26468		162	5734.28	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	7252.02
1.26579	Low confidence	152	4660.09		5898.71
1.26808		151	410.457	williams-beuren syndrome critical region protein 20 copy b. [refseq;acc:nm_145645]	323.685
1.26852		150	410.28	williams beuren syndrome chromosome region 20c isoform 1. [refseq;acc:nm_032158]	323.433
1.26875		149	745.137	glycine cleavage system h protein, mitochondrial precursor. [swissprot;acc:p23434]	945.391
1.26947		148	409.972	williams beuren syndrome critical region 20a isoform 2; nol1/nop2/sun gene family member; williams-beuren syndrome critical region protein 20 copy a; williams beuren syndrome chromosome region 20. [refseq;acc:nm_018044]	322.947
1.27473	High confidence	161	903.767	glycine cleavage system h protein, mitochondrial precursor. [swissprot;acc:p23434]	1152.06
1.27566		160	1653.74	huntingtin interacting protein c. [refseq;acc:nm_012272]	1296.38
1.27796		159	734.025	lipocalin-interacting membrane receptor. [refseq;acc:nm_018113]	574.372
1.28372	Low confidence	147	1310	gaba-a receptor-associated protein. [sptrembl;acc:q9by60]	1681.67
1.28508	High confidence	158	1283.48	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]	1649.37
1.28522	Low confidence	146	1073.89	adenosine deaminase (ec 3.5.4.4) (adenosine aminohydrolase). [swissprot;acc:p00813]	835.57
1.28761		145	553.827	lipocalin-interacting membrane receptor. [refseq;acc:nm_018113]	430.121
1.2878		144	749.494	associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799]	965.202
1.28908	High confidence	157	261.105	mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476]	336.584
	Low confidence	143
1.28932	High confidence	151	2230.13	udp-glucuronosyltransferase 2b17 precursor, microsomal (ec 2.4.1.17) (udpgt) (c19-steroid specific udp-glucuronosyltransferase). [swissprot;acc:o75795]	1729.7
		152		udp-glucuronosyltransferase 2b11 precursor, microsomal (ec 2.4.1.17) (udpgt). [swissprot;acc:o75310]
		153		udp-glucuronosyltransferase 2b4 precursor, microsomal (ec 2.4.1.17) (udpgt) (hyodeoxycholic acid) (hlug25) (udpgth-1). [swissprot;acc:p06133]

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.