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 544 to 593 of 3228 in total

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

Rank	description	red	green	network_comparison
544	rac-gamma serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-gamma) (protein kinase akt-3) (protein kinase b, gamma) (pkb gamma) (stk-2). [swissprot;acc:q9y243]	3889.27	4426.74	1.13819
545	rac-beta serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-beta) (protein kinase akt-2) (protein kinase b, beta) (pkb beta). [swissprot;acc:p31751]
546	zinc finger protein t86. [swissprot;acc:o00488]	4052.77	4612.54	1.13812
547	werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [refseq;acc:nm_020135]	5291.92	6020.19	1.13762
548	adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [swissprot;acc:p10109]	8268.19	9405.85	1.13759
549	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]	5865.79	6671.23	1.13731
550	prohibitin. [swissprot;acc:p35232]	5773.45	6563.69	1.13687
551	repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273]
552	cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240]	15427.2	13572.8	1.13663
553	tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [refseq;acc:nm_014886]	3853.64	4379.71	1.13651
554	pre-mrna cleavage complex ii protein clp1. [swissprot;acc:q92989]	14830.5	13050.3	1.13641
555	selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611]	6167.93	7007.7	1.13615
556	flavoprotein oxidoreductase mical2. [refseq;acc:nm_014632]
557	inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [refseq;acc:nm_003866]
558	selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [swissprot;acc:p49903]
559	inositol polyphosphate-4-phosphatase, type 1 isoform b; inositol polyphosphate-4-phosphatase, type i, 107kd; 4-phosphatase i; inositol polyphosphate-4-phosphatase i. [refseq;acc:nm_001566]
560	cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520]	5480.24	6222.04	1.13536
561	transforming protein rhoc (h9). [swissprot;acc:p08134]
562	thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762]
563	3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325]
564	transforming protein rhoa (h12). [swissprot;acc:p06749]
565	small glutamine-rich tetratricopeptide repeat-containing protein (vpu-binding protein) (ubp). [swissprot;acc:o43765]	10434.4	11846.2	1.1353
566	autoantigen ngp-1. [swissprot;acc:q13823]	3766.14	4274.79	1.13506
567	deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial precursor (ec 3.6.1.23) (dutpase) (dutp pyrophosphatase). [swissprot;acc:p33316]	10264.9	9043.51
568	grpe protein homolog 2, mitochondrial precursor (mt-grpe#2). [swissprot;acc:q8taa5]	4134.77	4691.24	1.13458
569	grpe protein homolog 1, mitochondrial precursor (mt-grpe#1) (hmge). [swissprot;acc:q9hav7]
570	swi/snf-related matrix-associated actin-dependent regulator of chromatin d2; rsc6p; mammalian chromatin remodeling complex brg1-associated factor 60b; swp73-like protein; chromatin remodeling complex baf60b subunit; swi/snf complex 60 kda subunit b. [refseq;acc:nm_003077]
571	swi/snf-related matrix-associated actin-dependent regulator of chromatin d3; rsc6p; mammalian chromatin remodeling complex brg1-associated factor 60c; swp73-like protein; chromatin remodeling complex baf60c subunit; swi/snf complex 60 kda subunit c. [refseq;acc:nm_003078]
572	swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily d member 1 (swi/snf complex 60 kda subunit) (brg1- associated factor 60a). [swissprot;acc:q96gm5]
573	homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [swissprot;acc:p31260]	6739.43	7644.55	1.1343
574	homeobox protein hox-b9 (hox-2e) (hox-2.5). [swissprot;acc:p17482]	6739.61	7644.58	1.13428
575	homeobox protein hox-a9 (hox-1g). [swissprot;acc:p31269]	6739.63	7644.59	1.13427
576	homeobox protein hox-c9 (hox-3b). [swissprot;acc:p31274]	6739.7	7644.6	1.13426
577	gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [swissprot;acc:q99928]	6739.81	7644.62	1.13425
578	forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488]
579	gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [swissprot;acc:q8n1c3]	6739.82
580	gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p47869]	6739.83	7644.63
581	gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [swissprot;acc:q16445]	6739.82
582	gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p18507]		7644.62
583	interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123]	6739.81
584	gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [swissprot;acc:p48169]	6739.82	7644.63
585	gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334]
586	phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167]	6739.81	7644.62
587	gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [swissprot;acc:p14867]	6739.83	7644.63
588	gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [swissprot;acc:p34903]
589	nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [swissprot;acc:p56556]	6739.85		1.13424
590	similar to expressed sequence aa415817. [sptrembl;acc:q8n4q9]
591	homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356]	6740.5	7644.76	1.13415
592	histone h2b.c (h2b/c). [swissprot;acc:q99880]	3946.32	4475.47	1.13409
593	histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778]

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.