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	Value Type	Gene	description	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	Value Type	description	red	network_comparison	green
13	Squared	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]	37.5863	10.3414	388.696
	Rooted		19.9625	1.79326	35.798
14	Measured	ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2]	398.5	3.21581	1281.5
	Ranked	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	56.6768	1.32952	75.3531
	Squared	ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2]	37.5863	10.3414	388.696
	Rooted		19.9625	1.79326	35.798
15	Measured	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	2671	3.06659	871
	Ranked	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8]	56.7244	1.32914	75.3948
	Squared	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	1688.58	9.40399	179.56
	Rooted	gbp protein isoform a. [refseq;acc:nm_017870]	23.9771	1.77158	42.4773
16	Measured	protein x 0004. [refseq;acc:nm_016301]	2671	3.06659	871
	Ranked	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492]	56.7252	1.32913	75.3954
	Squared	protein x 0004. [refseq;acc:nm_016301]	1688.58	9.40399	179.56
	Rooted	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	51.6817	1.75117	29.5127
17	Measured	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8]	460	2.96739	1365
	Ranked	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	56.7841	1.32866	75.447
	Squared	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8]	50.0828	8.80542	441
	Rooted	protein x 0004. [refseq;acc:nm_016301]	51.6817	1.75117	29.5127
18	Measured	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	677.5	2.75351	1865.5
	Ranked	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	185.678	1.32082	245.247
	Squared	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	108.641	7.58176	823.69
	Rooted	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8]	21.4476	1.72261	36.9459
19	Measured	microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	677.5	2.75351	1865.5
	Ranked	glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216]	185.678	1.32082	245.247
	Squared	microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	108.641	7.58176	823.69
	Rooted	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]	25.6987	1.69507	43.561
20	Measured	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]	677.5	2.75351	1865.5
	Ranked	glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737]	185.678	1.32082	245.247
	Squared	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]	108.641	7.58176	823.69
	Rooted	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262]	40.3337	1.66157	24.2744
21	Measured	ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485]	677.5	2.75351	1865.5
	Ranked	myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7]	185.678	1.32082	245.247
	Squared	ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485]	108.641	7.58176	823.69
	Rooted	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6]	40.3337	1.66157	24.2744
22	Measured	protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]	677.5	2.75351	1865.5
	Ranked	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217]	185.678	1.32082	245.247
	Squared	protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]	108.641	7.58176	823.69
	Rooted	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150]	40.3357	1.66049	24.2915
23	Measured	gbp protein isoform a. [refseq;acc:nm_017870]	699.76	2.7072	1894.39
	Ranked	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	58	1.31818	44
	Squared	neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784]	143.692	3.18404	457.521
	Rooted	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798]	40.3358	1.66046	24.2919
24	Measured	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]	950.561	2.21818	2108.52
	Ranked	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]	58	1.31818	44
	Squared	chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873]	143.692	3.18404	457.521
	Rooted	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08]	40.336	1.66032	24.2941
25	Measured	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262]	1833.01	2.0534	892.67
	Ranked	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]	58	1.31818	44
	Squared	doc-1 related protein (doc-1r). [swissprot;acc:o75956]	143.692	3.18404	457.521
	Rooted	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670]	40.3361	1.66026	24.295

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.