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	network_comparison	red	green

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Showing element 51 to 100 of 12912 in total

Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Value Type	network_comparison	red	green
13	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]	Rooted	1.79326	19.9625	35.798
	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	Ranked	1.3585	288.754	212.554
14	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]		1.32952	56.6768	75.3531
	ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2]	Measured	3.21581	398.5	1281.5
		Squared	10.3414	37.5863	388.696
		Rooted	1.79326	19.9625	35.798
15	gbp protein isoform a. [refseq;acc:nm_017870]		1.77158	23.9771	42.4773
	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8]	Ranked	1.32914	56.7244	75.3948
	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	Measured	3.06659	2671	871
		Squared	9.40399	1688.58	179.56
16	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492]	Ranked	1.32913	56.7252	75.3954
	protein x 0004. [refseq;acc:nm_016301]	Measured	3.06659	2671	871
		Squared	9.40399	1688.58	179.56
	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	Rooted	1.75117	51.6817	29.5127
17	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	Ranked	1.32866	56.7841	75.447
	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8]	Measured	2.96739	460	1365
		Squared	8.80542	50.0828	441
	protein x 0004. [refseq;acc:nm_016301]	Rooted	1.75117	51.6817	29.5127
18	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	Ranked	1.32082	185.678	245.247
	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8]	Rooted	1.72261	21.4476	36.9459
	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	Measured	2.75351	677.5	1865.5
		Squared	7.58176	108.641	823.69
19	glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216]	Ranked	1.32082	185.678	245.247
	microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	Measured	2.75351	677.5	1865.5
		Squared	7.58176	108.641	823.69
	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]	Rooted	1.69507	25.6987	43.561
20	glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737]	Ranked	1.32082	185.678	245.247
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262]	Rooted	1.66157	40.3337	24.2744
	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]	Measured	2.75351	677.5	1865.5
		Squared	7.58176	108.641	823.69
21	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	2.75351	677.5	1865.5
		Squared	7.58176	108.641	823.69
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6]	Rooted	1.66157	40.3337	24.2744
	myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7]	Ranked	1.32082	185.678	245.247
22	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217]
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150]	Rooted	1.66049	40.3357	24.2915
	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	2.75351	677.5	1865.5
		Squared	7.58176	108.641	823.69
23	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	Ranked	1.31818	58	44
	gbp protein isoform a. [refseq;acc:nm_017870]	Measured	2.7072	699.76	1894.39
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798]	Rooted	1.66046	40.3358	24.2919
	neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784]	Squared	3.18404	143.692	457.521
24	chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873]
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08]	Rooted	1.66032	40.336	24.2941
	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]	Ranked	1.31818	58	44
	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]	Measured	2.21818	950.561	2108.52
25	doc-1 related protein (doc-1r). [swissprot;acc:o75956]	Squared	3.18404	143.692	457.521
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670]	Rooted	1.66026	40.3361	24.295
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262]	Measured	2.0534	1833.01	892.67
	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]	Ranked	1.31818	58	44

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.