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	Interaction Map	Network Comparison Type	red	Filtered	green	network_comparison

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Showing element 101 to 150 of 14920 in total

Interaction Map  : High confidence
Network Comparison Type  : Divided

Rank	description	Value Type	red	Filtered	green	network_comparison
13	dok-like protein. [refseq;acc:nm_024872]	Squared	0.289941	0	0.00001	28994.1
		Rooted	5.91608			591608
	heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107]	Ranked	5210.5		9264.5	1.77804
	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]		288.754	1	212.554	1.3585
14	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	Squared	1.73869	0	19295.9	11098
	cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]	Measured	130.512		6.50325	20.0687
	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	Ranked	56.6768	1	75.3531	1.32952
	dystrophin. [swissprot;acc:p11532]		10232.5	0	18054.8	1.76446
	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	0.00001		4.24264	424264
	ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2]	Measured	398.5	1	1281.5	3.21581
		Squared	37.5863		388.696	10.3414
		Rooted	19.9625		35.798	1.79326
15	gbp protein isoform a. [refseq;acc:nm_017870]		23.9771		42.4773	1.77158
	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	Squared	1.73869	0	19295.9	11098
	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8]	Ranked	56.7244	1	75.3948	1.32914
	rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372]	Rooted	4.24264	0	0.00001	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	10		156	15.6
		Ranked	19403		11267	1.72211
	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	Measured	2671	1	871	3.06659
		Squared	1688.58		179.56	9.40399
16	cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]	Ranked	12170.7	0	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]		56.7252	1	75.3954	1.32913
	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	0.00001	0	0.0766864	7668.64
	protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992]	Measured	1		15	15
	protein x 0004. [refseq;acc:nm_016301]		2671	1	871	3.06659
		Squared	1688.58		179.56	9.40399
	serpin b12. [swissprot;acc:q96p63]	Rooted	10.2928	0	1.18697	8.67149
	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]		51.6817	1	29.5127	1.75117
17	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	Ranked	56.7841		75.447	1.32866
	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8]	Measured	460		1365	2.96739
		Squared	50.0828		441	8.80542
	fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402]	Ranked	11543	0	6812	1.69451
	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	Rooted	10.3085		1.2188	8.45791
	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	Measured	859		58	14.8103
	protein x 0004. [refseq;acc:nm_016301]	Rooted	51.6817	1	29.5127	1.75117
	rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372]	Squared	0.0766864	0	0.00001	7668.64
18	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	Ranked	185.678	1	245.247	1.32082
	60s ribosomal protein l37a. [swissprot;acc:p12751]	Measured	305.45	0	26.1599	11.6763
	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	Squared	439.709		0.52284	841.001
	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	Rooted	9.20014		60.0707	6.52932
	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8]		21.4476	1	36.9459	1.72261
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Ranked	22286	0	13216	1.68629
	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	Measured	677.5	1	1865.5	2.75351
		Squared	108.641		823.69	7.58176
19	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]	Measured	305.45	0	26.1599	11.6763
	glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216]	Ranked	185.678	1	245.247	1.32082
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]		22286	0	13216	1.68629
	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	Rooted	9.20014		60.0707	6.52932
	microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	Measured	677.5	1	1865.5	2.75351
		Squared	108.641		823.69	7.58176

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.