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	Filtered	Interaction Map	green	red	network_comparison

Results: HTML CSV LaTeX

Showing element 51 to 100 of 8289 in total

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

Rank	description	Interaction Map	green	red	network_comparison
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	286.347	1.20085
	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]	High confidence	44	58	1.31818
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	284.798	1.19792
	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	High confidence	44	58	1.31818
28	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]	Low confidence	170	142	1.19718
	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847]	High confidence	153.671	201.949	1.31416
29		Low confidence	170.557	203.115	1.19089
	uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48]	High confidence	243.678	187.458	1.29991
30	bcl2-related ovarian killer. [refseq;acc:nm_032515]	Low confidence	223.235	265.638	1.18995
	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	187.457	1.29991
31	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]	Low confidence	48.8186	57.395	1.17568
	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	187.458	1.2999
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	273.188	1.17505
	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	187.462	1.29985
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	210.241	1.17068
	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	188.688	1.28647
34	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	Low confidence	133.876	155.56	1.16197
	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	189.07	1.28235
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	260.532	1.27519
	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	Low confidence	258.59	297.273	1.14959
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	260.532	1.27519
	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	Low confidence	258.33	296.837	1.14906
37	chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0]		217.843	250.244	1.14874
	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	High confidence	253	322	1.27273
38	glucosamine-6-phosphate isomerase. [refseq;acc:nm_138335]	Low confidence	282.937	247.202	1.14456
	microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	High confidence	253	322	1.27273
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	247.202	1.14456
	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]	High confidence	253	322	1.27273
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	255.382	1.14245
41	ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5]		200.55	228.147	1.13761
	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	322	1.27273
42	glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417]	Low confidence	200.532	227.371	1.13384
	proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100]	High confidence	160.957	204.641	1.2714
43	jun dimerization protein. [refseq;acc:nm_130469]
	regulator of g-protein signaling 12 (rgs12). [swissprot;acc:o14924]	Low confidence	219.841	247.768	1.12703
44	fos-related antigen 2. [swissprot;acc:p15408]	High confidence	161.046	204.641	1.2707
	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	Low confidence	217.217	242.742	1.11751
45	microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]
	protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539]	High confidence	161.051	204.641	1.27066
46	fos-related antigen 1 (fra-1). [swissprot;acc:p15407]		161.068	204.642	1.27053
	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]	Low confidence	217.217	242.742	1.11751
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	325.586	1.26938
48	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278]		83.0461	65.4586	1.26868
	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	242.742	1.11751
49	beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121]	High confidence	105	133	1.26667
	t-box transcription factor tbx19 (t-box protein 19). [swissprot;acc:o60806]	Low confidence	202.569	225.438	1.11289
50	beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]	High confidence	105	133	1.26667
	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	Low confidence	260.98	234.802	1.11149

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.