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 7812 to 7861 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
489	disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6]	Rooted	Subtracted	1	62.7424	67.9648	5.2224
	dj579f20.1 (high-mobility group (nonhistone chromosomal) protein 1-like 1). [sptrembl;acc:q9nqj4]	Measured	Divided	0	22946.3	22895.1	1.00224
	glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 1 (ec 2.6.1.16) (hexosephosphate aminotransferase 1) (d-fructose-6- phosphate amidotransferase 1) (gfat 1) (gfat1). [swissprot;acc:q06210]	Rooted			22.997	22.9676	1.00128
			Subtracted				0.0294
	kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719]	Squared	Divided		21555.6	21619.8	1.00298
	likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745]	Ranked			8854.04	8811.09	1.00487
	phosphatidate cytidylyltransferase 2 (ec 2.7.7.41) (cdp-diglyceride synthetase 2) (cdp-diglyceride pyrophosphorylase 2) (cdp- diacylglycerol synthase 2) (cds 2) (ctp:phosphatidate cytidylyltransferase 2) (cdp-dag synthase 2) (cdp-dg synthetase 2). [swissprot;acc:o95674]	Squared		1	26859	32321.2	1.20337
	protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688]	Ranked			231.276	215.627	1.07257
	protocadherin 16 precursor (cadherin 19) (cadherin fibroblast 1). [swissprot;acc:q96jq0]	Measured	Subtracted	0	14	11.5	2.5
		Squared			0.092781	0.0318343	0.0609467
	pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322]	Measured	Divided	1	5281.11	6044.61	1.14457
	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]	Ranked	Subtracted	0	6802.96	6829.74	26.78
	vesicle-associated membrane protein 1 (vamp-1) (synaptobrevin 1). [swissprot;acc:p23763]	Squared		1	27516.2	32720	5203.8
490	arsenical pump-driving atpase (ec 3.6.3.16) (arsenite-translocating atpase) (arsenical resistance atpase) (arsenite-transporting atpase) (arsa) (asna-i). [swissprot;acc:o43681]	Rooted	Divided	0	24.4309	24.4079	1.00094
			Subtracted				0.023
	dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0]	Ranked	Divided		10388.7	10338.7	1.00484
		Squared			3228.32	3221.55	1.0021
	ferritin light chain (ferritin l subunit). [swissprot;acc:p02792]	Rooted	Subtracted	1	62.7424	67.9648	5.2224
	forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457]	Squared	Divided		5301.97	6377.93	1.20294
	high mobility group protein 1-like 10 (hmg-1l10). [swissprot;acc:q9ugv6]	Measured		0	22940.1	22888.8	1.00224
	histidine decarboxylase (ec 4.1.1.22) (hdc). [swissprot;acc:p19113]		Subtracted	1	7101.94	7949.84	847.9
	lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455]	Ranked			242.531	227.136	15.395
	nudix (nucleoside diphosphate linked moiety x)-type motif 12. [refseq;acc:nm_031438]	Rooted	Divided		50.5505	46.2797	1.09228
	protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316]	Measured			15274.9	13346.9	1.14445
	protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992]	Squared	Subtracted	0	0.000236686	0.0532544	0.0530177
	rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [swissprot;acc:q14155]	Ranked	Divided	1	220.183	236.015	1.0719
	signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240]		Subtracted	0	11985.5	11959.4	26.1
	transcription factor btf3 homolog 3. [swissprot;acc:q13892]	Measured			219.759	221.565	1.806
	vesicule-associated membrane protein 4 (vamp-4). [swissprot;acc:o75379]	Squared		1	27516.2	32720	5203.8
491	adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559]			0	0.125207	0.0854438	0.0397632
	cdp-diacylglycerol--inositol 3-phosphatidyltransferase (ec 2.7.8.11) (phosphatidylinositol synthase) (ptdins synthase) (pi synthase). [swissprot;acc:o14735]			1	27516.2	32720	5203.8
	clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675]	Rooted	Divided	0	42.6139	42.6315	1.00041
			Subtracted				0.0176
	disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [swissprot;acc:q9y2h0]			1	62.7424	67.9648	5.2224
	forkhead box protein p1 (hspc215). [swissprot;acc:q9h334]	Squared	Divided		5302.25	6378.24	1.20293
	high mobility group protein 1 (hmg-1). [swissprot;acc:p09429]	Measured		0	22962	22910.9	1.00223
	metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889]	Ranked	Subtracted	1	150.959	166.351	15.392
	neuron navigator 2 isoform l; retinoic acid inducible in neuroblastoma; pore membrane and/or filament interacting like protein 2; helicase helad1. [refseq;acc:nm_145117]	Measured	Divided		5980.15	6843.48	1.14437
	nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4]	Ranked			251.83	234.951	1.07184
	parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [refseq;acc:nm_004562]	Rooted			55.1759	60.2621	1.09218
	probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185]	Squared		0	2871.07	2873.96	1.00101
	pyruvate dehydrogenase e1 component alpha subunit, testis-specific form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type ii). [swissprot;acc:p29803]	Measured	Subtracted		2410.35	2411.78	1.43
	rwd domain containing 1; ptd013 protein; cgi-24 protein. [refseq;acc:nm_015952]	Ranked	Divided		21970	21880	1.00411
	sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633]		Subtracted		13692.7	13718.2	25.5
	sh3-containing grb2-like protein 3 (sh3 domain protein 2c) (een-b2). [swissprot;acc:q99963]	Measured		1	7067.46	7909.27	841.81
492	3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8]		Divided	0	5038.33	5046.33	1.00159
	4-aminobutyrate aminotransferase, mitochondrial precursor (ec 2.6.1.19) (gamma-amino-n-butyrate transaminase) (gaba transaminase) (gaba aminotransferase) (gaba-at) (gaba-t). [swissprot;acc:p80404]	Squared	Subtracted		0.108639	0.145878	0.037239
	adp-ribosylation factor gtpase activating protein 1 (adp-ribosylation factor 1 gtpase activating protein) (arf1 gap) (arf1-directed gtpase- activating protein) (gap protein). [swissprot;acc:q8n6t3]			1	27516.2	32720	5203.8
	beta-1,4 mannosyltransferase. [refseq;acc:nm_019109]	Ranked			150.982	166.372	15.39
	dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8]	Squared	Divided	0	6791.15	6792.32	1.00017

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.