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	Value Type	description	Filtered	Network Comparison Type	Interaction Map	green	network_comparison	red

Results: HTML CSV LaTeX

Showing element 51 to 100 of 8289 in total

Value Type  : Ranked
Filtered  : 1
Network Comparison Type  : Divided

Rank	description	Interaction Map	green	network_comparison	red
26	cytochrome p450 27, mitochondrial precursor (ec 1.14.-.-) (cytochrome p-450c27/25) (sterol 26-hydroxylase) (sterol 27-hydroxylase) (vitamin d(3) 25-hydroxylase) (5-beta-cholestane-3-alpha,7-alpha,12-alpha-triol 27-hydroxylase). [swissprot;acc:q02318]	Low confidence	238.454	1.20085	286.347
	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]	High confidence	44	1.31818	58
27	cytochrome p450 24a1, mitochondrial precursor (ec 1.14.-.-) (p450- cc24) (vitamin d(3) 24-hydroxylase) (1,25-dihydroxyvitamin d(3) 24- hydroxylase) (24-ohase). [swissprot;acc:q07973]	Low confidence	237.743	1.19792	284.798
	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	High confidence	44	1.31818	58
28	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]	Low confidence	170	1.19718	142
	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847]	High confidence	153.671	1.31416	201.949
29		Low confidence	170.557	1.19089	203.115
	uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48]	High confidence	243.678	1.29991	187.458
30	bcl2-related ovarian killer. [refseq;acc:nm_032515]	Low confidence	223.235	1.18995	265.638
	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [swissprot;acc:q00007]	High confidence	243.678	1.29991	187.457
31	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]	Low confidence	48.8186	1.17568	57.395
	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [swissprot;acc:q00005]	High confidence	243.677	1.2999	187.458
32	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]	Low confidence	232.49	1.17505	273.188
	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]	High confidence	243.673	1.29985	187.462
33	dual specificity mitogen-activated protein kinase kinase 4 (ec 2.7.1.-) (map kinase kinase 4) (jnk activating kinase 1) (c-jun n- terminal kinase kinase 1) (jnkk) (sapk/erk kinase 1) (sek1). [swissprot;acc:p45985]	Low confidence	246.125	1.17068	210.241
	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]	High confidence	242.742	1.28647	188.688
34	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	Low confidence	133.876	1.16197	155.56
	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]	High confidence	242.453	1.28235	189.07
35	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]		204.309	1.27519	260.532
	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	Low confidence	258.59	1.14959	297.273
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]	High confidence	204.309	1.27519	260.532
	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	Low confidence	258.33	1.14906	296.837
37	chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0]		217.843	1.14874	250.244
	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	High confidence	253	1.27273	322
38	glucosamine-6-phosphate isomerase. [refseq;acc:nm_138335]	Low confidence	282.937	1.14456	247.202
	microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	High confidence	253	1.27273	322
39	glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926]	Low confidence	282.937	1.14456	247.202
	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]	High confidence	253	1.27273	322
40	ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485]
	son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583]	Low confidence	223.538	1.14245	255.382
41	ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5]		200.55	1.13761	228.147
	protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]	High confidence	253	1.27273	322
42	glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417]	Low confidence	200.532	1.13384	227.371
	proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100]	High confidence	160.957	1.2714	204.641
43	jun dimerization protein. [refseq;acc:nm_130469]
	regulator of g-protein signaling 12 (rgs12). [swissprot;acc:o14924]	Low confidence	219.841	1.12703	247.768
44	fos-related antigen 2. [swissprot;acc:p15408]	High confidence	161.046	1.2707	204.641
	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	Low confidence	217.217	1.11751	242.742
45	microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]
	protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539]	High confidence	161.051	1.27066	204.641
46	fos-related antigen 1 (fra-1). [swissprot;acc:p15407]		161.068	1.27053	204.642
	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]	Low confidence	217.217	1.11751	242.742
47	ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485]
	gbp protein isoform a. [refseq;acc:nm_017870]	High confidence	256.492	1.26938	325.586
48	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278]		83.0461	1.26868	65.4586
	protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]	Low confidence	217.217	1.11751	242.742
49	beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121]	High confidence	105	1.26667	133
	t-box transcription factor tbx19 (t-box protein 19). [swissprot;acc:o60806]	Low confidence	202.569	1.11289	225.438
50	beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]	High confidence	105	1.26667	133
	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	Low confidence	260.98	1.11149	234.802

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.