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	Value Type	Network Comparison Type	Interaction Map	Filtered	red	green	network_comparison

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Showing element 2225 to 2274 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
140	20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298]	Ranked	Subtracted	1	228.306	198.011	30.295
	alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7]	Rooted	Divided	0	25.8457	21.7945	1.18588
	cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941]	Squared		1	81527.6	56190.6	1.45091
	dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743]	Ranked	Subtracted	0	15081.8	16802.1	1720.3
	filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [refseq;acc:nm_001457]	Rooted	Divided	1	55.6161	66.7332	1.19989
	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	Measured	Subtracted		2597.5	698.5	1899
	kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193]		Divided		2760.28	2100.27	1.31425
	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]	Ranked		0	16411.9	14027.1	1.17001
	mto1 protein homolog (cgi-02). [swissprot;acc:q9y2z2]	Squared			677.989	382.311	1.7734
	protein kinase c, eta type (ec 2.7.1.-) (npkc-eta) (pkc-l). [swissprot;acc:p24723]		Subtracted	1	86609.4	65234.5	21374.9
	ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570]	Ranked	Divided		59	49	1.20408
	sad1/unc-84 protein-like 1. [swissprot;acc:o94901]	Rooted	Subtracted		39.9725	52.9973	13.0248
	sal-like protein 4 (zinc finger protein sall4). [swissprot;acc:q9ujq4]			0	30.2675	34.1662	3.8987
	scratch; scratch 1. [refseq;acc:nm_031309]	Squared			5976.46	5135.5	840.96
	tigger transposable element derived 6. [refseq;acc:nm_030953]	Measured			202.374	438.605	236.231
	vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [swissprot;acc:o95670]		Divided		934.726	1222.89	1.30829
141	associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799]	Rooted	Subtracted	1	105.205	92.2415	12.9635
	bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340]	Squared	Divided	0	15.0305	26.5621	1.76721
	cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747]	Ranked	Subtracted	1	239.991	269.238	29.247
	ccr4-not transcription complex, subunit 7 (ccr4-associated factor 1) (caf1) (btg1 binding factor 1). [swissprot;acc:q9uiv1]	Measured	Divided	0	1161.88	891.114	1.30385
	daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959]	Rooted	Subtracted		23.9877	20.1222	3.8655
	dj470l14.3 (novel protein similar to the arp2/3 protein complex subunit p21-arc (arc21)). [sptrembl;acc:q9h5b6]	Squared			5127.13	5964.46	837.33
	g2/mitotic-specific cyclin b1. [swissprot;acc:p14635]		Divided	1	81520.8	56188.5	1.45084
	hbs1-like. [refseq;acc:nm_006620]	Measured	Subtracted		2597.5	698.5	1899
	lamin b2. [swissprot;acc:q03252]	Rooted	Divided	0	17.4452	14.7595	1.18196
	probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185]	Ranked			7690.02	8991.19	1.1692
	protein kinase c, epsilon type (ec 2.7.1.-) (npkc-epsilon). [swissprot;acc:q02156]	Squared	Subtracted	1	86600.9	65229.9	21371
	ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157]	Ranked	Divided		59	49	1.20408
	rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316]	Rooted			55.6161	66.7332	1.19989
	small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330]	Measured			4405.4	5782.08	1.3125
	tigger transposable element derived 7; jerky (mouse) homolog-like. [refseq;acc:nm_033208]		Subtracted	0	202.163	438.035	235.872
	trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317]	Ranked			9411.34	11119.7	1708.36
142	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]	Rooted	Divided		21.0926	17.849	1.18172
	casein kinase i alpha s-like. [refseq;acc:nm_145203]		Subtracted		35.3509	31.4916	3.8593
	cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493]	Squared	Divided	1	81478.9	56175.2	1.45044
	dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03]		Subtracted	0	5936.62	5112.71	823.91
	heat shock factor binding protein 1. [swissprot;acc:o75506]		Divided		3647.42	2072.05	1.7603
	metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889]	Measured		1	9276.47	7090.37	1.30832
	peptidyl-prolyl cis-trans isomerase b precursor (ec 5.2.1.8) (ppiase) (rotamase) (cyclophilin b) (s-cyclophilin) (scylp) (cyp-s1). [swissprot;acc:p23284]	Squared	Subtracted		86600.9	65229.9	21371
	presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7]	Measured	Divided	0	874	1139	1.3032
	protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873]	Rooted		1	55.6161	66.7332	1.19989
	putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453]		Subtracted		105.205	92.2415	12.9635
	ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064]	Ranked	Divided		59	49	1.20408
	thrombospondin 3 precursor. [swissprot;acc:p49746]		Subtracted		239.99	269.234	29.244
	tigger transposable element derived 1; jerky (mouse) homolog-like. [refseq;acc:nm_145702]	Measured		0	202.156	438.016	235.86
	transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [swissprot;acc:p15884]	Ranked			16614	18296	1682
	transcription factor jun-d. [swissprot;acc:p17535]	Measured		1	5638.2	7523.39	1885.19
	voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02]	Ranked	Divided	0	8214.41	7026.41	1.16908
143	40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]	Measured	Subtracted		1499.4	1735.23	235.83
	anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685]	Ranked	Divided	1	59	49	1.20408

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.