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