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 2613 to 2662 of 6456 in total

Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Network Comparison Type	red	green	network_comparison
1307	calcipressin 3 (down syndrome candidate region 1-like protein 2) (myocyte-enriched calcineurin interacting protein 3) (mcip3). [swissprot;acc:q9uka8]	Subtracted	218.509	213.649	4.86
	serine/threonine protein phosphatase 2b catalytic subunit, beta isoform (ec 3.1.3.16) (calmodulin-dependent calcineurin a subunit, beta isoform) (cam-prp catalytic subunit). [swissprot;acc:p16299]	Divided	218.44	213.44	1.02343
1308	p protein (melanocyte-specific transporter protein). [swissprot;acc:q04671]			213.439
	werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [refseq;acc:nm_020135]	Subtracted	217.133	212.289	4.844
1309	exonuclease 1 isoform b; rad2 nuclease family member, homolog of s. cerevisiae exonuclease 1. [refseq;acc:nm_006027]		216.772	221.594	4.822
	prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [swissprot;acc:q15765]	Divided	226.439	221.26	1.02341
1310	phd finger protein 9. [refseq;acc:nm_018062]	Subtracted	216.772	221.594	4.822
	prefoldin subunit 2 (hspc231). [swissprot;acc:q9uhv9]	Divided	226.439	221.26	1.02341
1311	small optic lobes homolog; small optic lobes, drosophila, homolog of. [refseq;acc:nm_005632]	Subtracted	216.772	221.594	4.822
	uxt protein (ubiquitously expressed transcript protein) (hspc024). [swissprot;acc:q9ubk9]	Divided	226.439	221.26	1.02341
1312	n-acetylgalactosamine kinase (ec 2.7.1.-) (galnac kinase) (galactokinase 2). [swissprot;acc:q01415]	Subtracted	215.162	210.412	4.75
	rad50 homolog isoform 1. [refseq;acc:nm_005732]	Divided	199.739	204.407	1.02337
1313	galactose-1-phosphate uridylyltransferase (ec 2.7.7.12) (gal-1-p uridylyltransferase) (udp-glucose--hexose-1-phosphate uridylyltransferase). [swissprot;acc:p07902]	Subtracted	215.162	210.412	4.75
	signal transducer and activator of transcription 3 (acute-phase response factor). [swissprot;acc:p40763]	Divided	222.573	227.75	1.02326
1314	signal transducer and activator of transcription 4. [swissprot;acc:q14765]			227.751
	udp-glucose 4-epimerase (ec 5.1.3.2) (galactowaldenase) (udp- galactose 4-epimerase). [swissprot;acc:q14376]	Subtracted	215.162	210.412	4.75
1315	signal transducer and activator of transcription 1-alpha/beta (transcription factor isgf-3 components p91/p84). [swissprot;acc:p42224]	Divided	222.574	227.752	1.02326
	zinc finger protein zic 1 (zinc finger protein of the cerebellum 1). [swissprot;acc:q15915]	Subtracted	218.569	213.832	4.737
1316	signal transducer and activator of transcription 6 (il-4 stat). [swissprot;acc:p42226]	Divided	222.569	227.739	1.02323
	zinc finger protein zic 3 (zinc finger protein of the cerebellum 3). [swissprot;acc:o60481]	Subtracted	218.572	213.841	4.731
1317	centromere protein j; centrosomal p4.1-associated protein; lyst-interacting protein lip1; lag-3-associated protein. [refseq;acc:nm_018451]	Divided	206.773	202.105	1.0231
	zinc finger protein zic 2 (zinc finger protein of the cerebellum 2). [swissprot;acc:o95409]	Subtracted	218.574	213.847	4.727
1318	camp response element-binding protein cre-bpa. [refseq;acc:nm_004904]		218.591	213.899	4.692
	signal transducer and activator of transcription 5a. [swissprot;acc:p42229]	Divided	222.546	227.673	1.02304
1319	centromere protein j; centrosomal p4.1-associated protein; lyst-interacting protein lip1; lag-3-associated protein. [refseq;acc:nm_018451]	Subtracted	206.773	202.105	4.668
	glycogen [starch] synthase, muscle (ec 2.4.1.11). [swissprot;acc:p13807]	Divided	159.75	156.153	1.02304
1320	rad50 homolog isoform 1. [refseq;acc:nm_005732]	Subtracted	199.739	204.407	4.668
	signal transducer and activator of transcription 5b. [swissprot;acc:p51692]	Divided	222.544	227.667	1.02302
1321	m-phase inducer phosphatase 3 (ec 3.1.3.48) (dual specificity phosphatase cdc25c). [swissprot;acc:p30307]	Subtracted	259.439	254.797	4.642
	probable dimethyladenosine transferase (ec 2.1.1.-) (s- adenosylmethionine-6-n',n'-adenosyl(rrna) dimethyltransferase) (18s rrna dimethylase). [swissprot;acc:q9unq2]	Divided	226.347	221.259	1.023
1322	endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759]		159.86	156.275	1.02294
	suppressor of cytokine signaling 1 (socs-1) (jak-binding protein) (jab) (stat induced stat inhibitor 1) (ssi-1) (tec-interacting protein 3) (tip-3). [swissprot;acc:o15524]	Subtracted	216.542	211.908	4.634
1323	cytoplasmic protein nck2 (nck adaptor protein 2) (sh2/sh3 adaptor protein nck-beta) (nck-2). [swissprot;acc:o43639]	Divided	205.225	200.625	1.02293
	glia maturation factor gamma (gmf-gamma). [swissprot;acc:o60234]	Subtracted	216.542	211.908	4.634
1324	asc-1 complex subunit p100. [refseq;acc:nm_032204]
	glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840]	Divided	159.993	156.421	1.02284
1325	fk506-binding protein 1a (ec 5.2.1.8) (peptidyl-prolyl cis-trans isomerase) (ppiase) (rotamase) (12 kda fkbp) (fkbp-12) (immunophilin fkbp12). [swissprot;acc:p20071]	Subtracted	216.542	211.908	4.634
	werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [refseq;acc:nm_020135]	Divided	217.133	212.289	1.02282
1326	dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2]		218.509	213.648	1.02275
	upstream stimulatory factor 1 (major late transcription factor 1). [swissprot;acc:p22415]	Subtracted	214.987	210.359	4.628
1327	eyes absent homolog 3. [swissprot;acc:q99504]		218.537	213.91	4.627
	zinc finger protein zic 4 (zinc finger protein of the cerebellum 4) (fragment). [swissprot;acc:q8n9l1]	Divided	218.509	213.648	1.02275
1328	calcipressin 2 (thyroid hormone-responsive protein zaki-4) (down syndrome candidate region 1-like 1) (myocyte-enriched calcineurin interacting protein 2) (mcip2). [swissprot;acc:q14206]			213.649
	upstream stimulatory factor 2 (upstream transcription factor 2) (fos-interacting protein) (fip) (major late transcription factor 2). [swissprot;acc:q15853]	Subtracted	214.971	210.354	4.617
1329	cytoplasmic protein nck2 (nck adaptor protein 2) (sh2/sh3 adaptor protein nck-beta) (nck-2). [swissprot;acc:o43639]		205.225	200.625	4.6
	dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4v7]	Divided	218.509	213.648	1.02275
1330	calcipressin 1 (down syndrome critical region protein 1) (myocyte- enriched calcineurin interacting protein 1) (mcip1) (adapt78). [swissprot;acc:p53805]		218.508
	sal-like protein 2 (zinc finger protein sall2) (hsal2). [swissprot;acc:q9y467]	Subtracted	218.471	213.876	4.595
1331	arginine-glutamic acid dipeptide (re) repeats; atrophin 1-like; arginine glutamic acid dipeptide re repeats. [refseq;acc:nm_012102]		218.47	213.875
	calcipressin 3 (down syndrome candidate region 1-like protein 2) (myocyte-enriched calcineurin interacting protein 3) (mcip3). [swissprot;acc:q9uka8]	Divided	218.509	213.649	1.02275

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.