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

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Showing element 101 to 150 of 14920 in total

Network Comparison Type  : Divided
Interaction Map  : High confidence

Rank	Value Type	description	Filtered	red	green	network_comparison
13	Squared	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]	1	37.5863	388.696	10.3414
		dok-like protein. [refseq;acc:nm_024872]	0	0.289941	0.00001	28994.1
	Rooted	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]	1	19.9625	35.798	1.79326
		dok-like protein. [refseq;acc:nm_024872]	0	5.91608	0.00001	591608
14	Measured	cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]		130.512	6.50325	20.0687
		ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2]	1	398.5	1281.5	3.21581
	Ranked	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]		56.6768	75.3531	1.32952
		dystrophin. [swissprot;acc:p11532]	0	10232.5	18054.8	1.76446
	Squared	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]		1.73869	19295.9	11098
		ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2]	1	37.5863	388.696	10.3414
	Rooted	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]	0	0.00001	4.24264	424264
		ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2]	1	19.9625	35.798	1.79326
15	Measured	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]	0	10	156	15.6
		xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	1	2671	871	3.06659
	Ranked	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8]		56.7244	75.3948	1.32914
		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]	0	19403	11267	1.72211
	Squared	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]		1.73869	19295.9	11098
		xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	1	1688.58	179.56	9.40399
	Rooted	gbp protein isoform a. [refseq;acc:nm_017870]		23.9771	42.4773	1.77158
		rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372]	0	4.24264	0.00001	424264
16	Measured	protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992]		1	15	15
		protein x 0004. [refseq;acc:nm_016301]	1	2671	871	3.06659
	Ranked	cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]	0	12170.7	20670.6	1.69839
		microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492]	1	56.7252	75.3954	1.32913
	Squared	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]	0	0.00001	0.0766864	7668.64
		protein x 0004. [refseq;acc:nm_016301]	1	1688.58	179.56	9.40399
	Rooted	serpin b12. [swissprot;acc:q96p63]	0	10.2928	1.18697	8.67149
		xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	1	51.6817	29.5127	1.75117
17	Measured	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8]		460	1365	2.96739
		mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	0	859	58	14.8103
	Ranked	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	1	56.7841	75.447	1.32866
		fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402]	0	11543	6812	1.69451
	Squared	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8]	1	50.0828	441	8.80542
		rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372]	0	0.0766864	0.00001	7668.64
	Rooted	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]		10.3085	1.2188	8.45791
		protein x 0004. [refseq;acc:nm_016301]	1	51.6817	29.5127	1.75117
18	Measured	60s ribosomal protein l37a. [swissprot;acc:p12751]	0	305.45	26.1599	11.6763
		protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	1	677.5	1865.5	2.75351
	Ranked	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]		185.678	245.247	1.32082
		homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	0	22286	13216	1.68629
	Squared	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]		439.709	0.52284	841.001
		protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	1	108.641	823.69	7.58176
	Rooted	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	0	9.20014	60.0707	6.52932
		dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8]	1	21.4476	36.9459	1.72261
19	Measured	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]	0	305.45	26.1599	11.6763
		microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	1	677.5	1865.5	2.75351
	Ranked	glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216]		185.678	245.247	1.32082
		homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	0	22286	13216	1.68629
	Squared	microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	1	108.641	823.69	7.58176
		serpin b12. [swissprot;acc:q96p63]	0	23.5744	0.0289898	813.196

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.