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

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Showing element 201 to 250 of 38536 in total

Network Comparison Type  : Divided

Rank	Filtered	description	Value Type	Interaction Map	green	red	network_comparison
13	1	25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [swissprot;acc:o15528]	Rooted	Low confidence	52.5277	39.2301	1.33896
		carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976]	Squared		242799	395912	1.63062
		cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]	Measured	High confidence	1281.5	398.5	3.21581
			Squared		388.696	37.5863	10.3414
			Rooted		35.798	19.9625	1.79326
		jumonji domain containing 1; zinc finger protein; testis-specific protein a. [refseq;acc:nm_018433]	Measured	Low confidence	2959.19	1927.68	1.5351
		nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Ranked		29.1831	37.9984	1.30207
		protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]		High confidence	212.554	288.754	1.3585
14	0	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	Squared		19295.9	1.73869	11098
			Rooted	Low confidence	60.0707	9.20014	6.52932
		cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]	Measured	High confidence	6.50325	130.512	20.0687
		dystrophin. [swissprot;acc:p11532]	Ranked		18054.8	10232.5	1.76446
		guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [swissprot;acc:q9byb4]	Measured	Low confidence	59	0.00001	5900000
		mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	Squared		0.796213	174.646	219.346
		phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [swissprot;acc:o00750]	Rooted	High confidence	4.24264	0.00001	424264
		ptd016 protein. [refseq;acc:nm_016125]	Ranked	Low confidence	11234	18050	1.60673
	1	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]	Squared		4959.41	7744.68	1.56161
		cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	Ranked	High confidence	75.3531	56.6768	1.32952
		cytochrome p450 27, mitochondrial precursor (ec 1.14.-.-) (cytochrome p-450c27/25) (sterol 26-hydroxylase) (sterol 27-hydroxylase) (vitamin d(3) 25-hydroxylase) (5-beta-cholestane-3-alpha,7-alpha,12-alpha-triol 27-hydroxylase). [swissprot;acc:q02318]	Rooted	Low confidence	52.5401	39.2489	1.33864
		ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2]	Measured	High confidence	1281.5	398.5	3.21581
			Squared		388.696	37.5863	10.3414
			Rooted		35.798	19.9625	1.79326
		trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [swissprot;acc:p35030]	Measured	Low confidence	2998.1	1972.65	1.51983
		vitelliform macular dystrophy 2-like protein 1. [refseq;acc:nm_017682]	Ranked		29.1831	37.9984	1.30207
15	0	adenomatous polyposis coli like. [refseq;acc:nm_005883]			7597.61	12074.1	1.5892
		fk506-binding protein 6 (ec 5.2.1.8) (peptidyl-prolyl cis-trans isomerase) (ppiase) (rotamase) (36 kda fk506 binding protein) (fkbp- 36) (immunophilin fkbp36). [swissprot;acc:o75344]	Squared		5.80317	0.0279126	207.905
			Rooted		8.64796	2.24657	3.84941
		lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	Measured		2740.13	485.286	5.64642
			Squared	High confidence	19295.9	1.73869	11098
		rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372]	Rooted		0.00001	4.24264	424264
		succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [swissprot;acc:o14521]	Measured		156	10	15.6
			Ranked		11267	19403	1.72211
	1	cytochrome p450 24a1, mitochondrial precursor (ec 1.14.-.-) (p450- cc24) (vitamin d(3) 24-hydroxylase) (1,25-dihydroxyvitamin d(3) 24- hydroxylase) (24-ohase). [swissprot;acc:q07973]	Rooted	Low confidence	52.9343	39.8493	1.32836
		gbp protein isoform a. [refseq;acc:nm_017870]		High confidence	42.4773	23.9771	1.77158
		microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8]	Ranked		75.3948	56.7244	1.32914
		protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]		Low confidence	202.362	255.046	1.26035
		sperm associated antigen 7. [refseq;acc:nm_004890]	Squared		136572	209554	1.53438
		trypsin i precursor (ec 3.4.21.4) (cationic trypsinogen). [swissprot;acc:p07477]	Measured		3007.85	1983.91	1.51612
		xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]		High confidence	871	2671	3.06659
			Squared		179.56	1688.58	9.40399
16	0	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]	Ranked	Low confidence	11625	7395	1.57201
		cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]		High confidence	20670.6	12170.7	1.69839
		mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	Rooted	Low confidence	7.61577	29.3087	3.84842
		phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [swissprot;acc:o00750]	Squared	High confidence	0.0766864	0.00001	7668.64
		protein kinase, lysine deficient 3. [refseq;acc:nm_020922]	Measured	Low confidence	704.5	125	5.636
			Squared		221.042	4.89136	45.1903
		protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992]	Measured	High confidence	15	1	15
		serpin b12. [swissprot;acc:q96p63]	Rooted		1.18697	10.2928	8.67149
	1	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	Measured	Low confidence	28492	21185	1.34491
		bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090]	Squared		475119	333556	1.42441

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.