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 125 to 174 of 12912 in total

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

Rank	description	Value Type	red	green	network_comparison
32	beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]	Squared	9924.76	25146.6	2.53372
	ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485]	Rooted	26.0288	43.1914	1.65937
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8]	Measured	1834.73	895.893	2.04793
	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [swissprot;acc:q9y2t4]	Ranked	187.462	243.673	1.29985
33	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152]	Measured	1835.3	896.972	2.04611
	protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]	Rooted	26.0288	43.1914	1.65937
	serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, beta isoform (pp2a, subunit a, pr65-beta isoform) (pp2a, subunit a, r1-beta isoform). [swissprot;acc:p30154]	Ranked	188.688	242.742	1.28647
	spermatogenesis associated 6. [refseq;acc:nm_019073]	Squared	9924.76	25146.6	2.53372
34	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]
	guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992]	Measured	1836.71	907.546	2.02382
		Rooted	40.2812	24.3678	1.65305
	serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [swissprot;acc:p30153]	Ranked	189.07	242.453	1.28235
35	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	Squared	106226	192141	1.80879
	guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148]	Measured	1836.71	907.564	2.02378
		Rooted	40.2812	24.3679	1.65304
	nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952]	Ranked	260.532	204.309	1.27519
36	ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511]
	guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086]	Measured	1836.76	907.741	2.02344
		Rooted	40.2805	24.369	1.65294
	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]	Squared	106226	192141	1.80879
37	guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488]	Measured	1836.76	907.763	2.02339
		Rooted	40.2805	24.3691	1.65293
	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]	Squared	106226	192141	1.80879
	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	Ranked	322	253	1.27273
38	guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087]	Measured	1836.76	907.774	2.02337
		Rooted	40.2804	24.3692	1.65292
	microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	Ranked	322	253	1.27273
	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]	Squared	106226	192141	1.80879
39	guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899]	Measured	1836.8	907.903	2.02312
		Rooted	40.28	24.37	1.65285
	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	Squared	106226	192141	1.80879
	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]	Ranked	322	253	1.27273
40	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	Squared	144940	81169.7	1.78564
	ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485]	Ranked	322	253	1.27273
	guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898]	Measured	1836.81	907.978	2.02297
		Rooted	40.2797	24.3705	1.65281
41	guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754]	Measured	1836.81	907.978	2.02297
		Rooted	40.2797	24.3705	1.65281
	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8]	Squared	144912	81155	1.78562
	protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]	Ranked	322	253	1.27273
42	guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775]	Measured	1857.32	958.237	1.93827
		Rooted	40.225	24.7051	1.62821
	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492]	Squared	144911	81154.7	1.78561
	proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100]	Ranked	204.641	160.957	1.2714
43	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	Squared	144876	81136.5	1.78558
	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901]	Rooted	40.6302	25.4452	1.59677
	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520]	Measured	1881.02	1027.36	1.83093
	jun dimerization protein. [refseq;acc:nm_130469]	Ranked	204.641	160.957	1.2714
44	fos-related antigen 2. [swissprot;acc:p15408]			161.046	1.2707
	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278]	Squared	139741	78454.6	1.78117

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.