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 301 to 350 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
19	nucleoporin nup43 (p42). [swissprot;acc:q8nfh3]	Squared	Subtracted	0	10489.8	23426.5	12936.7
	phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086]	Rooted			23.8747	11.7898	12.0849
	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]		Divided	1	25.6987	43.561	1.69507
	serpin b12. [swissprot;acc:q96p63]	Squared		0	23.5744	0.0289898	813.196
20	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]	Rooted	Subtracted		23.8747	11.7898	12.0849
	cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]		Divided		11.3774	1.80368	6.30788
	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]		Subtracted	1	203.673	182.638	21.035
	ero1-like. [refseq;acc:nm_014584]	Measured	Divided	0	82	0.00001	8200000
	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278]		Subtracted	1	23421.5	17580.4	5841.1
	glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737]	Ranked	Divided		185.678	245.247	1.32082
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152]		Subtracted		266.868	336.159	69.291
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262]	Rooted	Divided		40.3337	24.2744	1.66157
	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Ranked		0	22286	13216	1.68629
	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	Squared			23.4957	0.0297673	789.312
	melanoma antigen, family b, 6. [refseq;acc:nm_173523]		Subtracted	1	219048	129762	89286
	polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361]	Measured		0	8763	7608	1155
	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]		Divided	1	677.5	1865.5	2.75351
		Squared			108.641	823.69	7.58176
	serpin b12. [swissprot;acc:q96p63]	Ranked	Subtracted	0	14604.2	21138.6	6534.4
	sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [swissprot;acc:p50993]	Squared			38799.5	25982	12817.5
21	acrc protein; putative nuclear protein. [refseq;acc:nm_052957]	Ranked	Divided		6313.38	10621.4	1.68236
		Rooted	Subtracted		44.2946	32.7593	11.5353
	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]		Divided		36.9188	6.85565	5.38516
	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]		Subtracted	1	153.602	133.195	20.407
	ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485]	Measured	Divided		677.5	1865.5	2.75351
		Squared			108.641	823.69	7.58176
	gbp protein isoform a. [refseq;acc:nm_017870]	Ranked	Subtracted		325.586	256.492	69.094
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6]	Rooted	Divided		40.3337	24.2744	1.66157
	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	Ranked	Subtracted	0	14592	21113.7	6521.7
	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	Measured		1	23693.7	18263	5430.7
	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]	Squared			219048	129762	89286
	myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7]	Ranked	Divided		185.678	245.247	1.32082
	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]	Squared		0	0.0236686	5.76	243.36
	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]	Measured	Subtracted		6804.88	5690.63	1114.25
		Squared			40674.4	28034.4	12640
	syntaxin 10 (syn10). [swissprot;acc:o60499]	Measured	Divided		118.878	17.6611	6.73106
22	cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336]	Rooted	Subtracted		24.454	13.5647	10.8893
	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217]	Ranked	Divided	1	185.678	245.247	1.32082
	glycogenin-2 (ec 2.4.1.186) (gn-2) (gn2). [swissprot;acc:o15488]	Squared	Subtracted	0	192242	204096	11854
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150]	Rooted	Divided	1	40.3357	24.2915	1.66049
	hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703]	Measured	Subtracted		23693.7	18263	5430.7
	melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]	Squared			219048	129762	89286
	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8]	Rooted			153.578	133.176	20.402
	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	Ranked			322	253	69
	protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]	Measured	Divided		677.5	1865.5	2.75351
		Squared			108.641	823.69	7.58176
	protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992]			0	0.000236686	0.0532544	225
	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	Ranked			20989	12479	1.68195
	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]	Measured			60	0.00001	6000000
	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]	Rooted			3.16228	12.49	3.94968

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.