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 75 to 124 of 8289 in total

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

Rank	description	Interaction Map	red	green	network_comparison
38	glucosamine-6-phosphate isomerase. [refseq;acc:nm_138335]	Low confidence	247.202	282.937	1.14456
	microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	High confidence	322	253	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	247.202	282.937	1.14456
	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]	High confidence	322	253	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	255.382	223.538	1.14245
41	ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5]		228.147	200.55	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	322	253	1.27273
42	glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417]	Low confidence	227.371	200.532	1.13384
	proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100]	High confidence	204.641	160.957	1.2714
43	jun dimerization protein. [refseq;acc:nm_130469]
	regulator of g-protein signaling 12 (rgs12). [swissprot;acc:o14924]	Low confidence	247.768	219.841	1.12703
44	fos-related antigen 2. [swissprot;acc:p15408]	High confidence	204.641	161.046	1.2707
	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	Low confidence	242.742	217.217	1.11751
45	microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]
	protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539]	High confidence	204.641	161.051	1.27066
46	fos-related antigen 1 (fra-1). [swissprot;acc:p15407]		204.642	161.068	1.27053
	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]	Low confidence	242.742	217.217	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	325.586	256.492	1.26938
48	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278]		65.4586	83.0461	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	242.742	217.217	1.11751
49	beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121]	High confidence	133	105	1.26667
	t-box transcription factor tbx19 (t-box protein 19). [swissprot;acc:o60806]	Low confidence	225.438	202.569	1.11289
50	beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]	High confidence	133	105	1.26667
	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	Low confidence	234.802	260.98	1.11149
51	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]
	spermatogenesis associated 6. [refseq;acc:nm_019073]	High confidence	133	105	1.26667
52	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]
	sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906]	Low confidence	234.802	260.98	1.11149
53	db83 protein. [swissprot;acc:p57088]
	transcription factor jun-b. [swissprot;acc:p17275]	High confidence	201.144	158.868	1.26611
54	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]	Low confidence	267.448	240.822	1.11056
	transcription factor jun-d. [swissprot;acc:p17535]	High confidence	200.941	158.941	1.26425
55	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	Low confidence	267.376	240.78	1.11046
	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]	High confidence	320.927	254.434	1.26134
56	brachyury protein (t protein). [swissprot;acc:o15178]	Low confidence	224.922	202.592	1.11022
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262]	High confidence	266.856	336.233	1.25998
57	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6]
	proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100]	Low confidence	202.802	182.73	1.10985
58	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150]	High confidence	266.863	336.191	1.25979
	jun dimerization protein. [refseq;acc:nm_130469]	Low confidence	202.802	182.73	1.10985
59	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798]	High confidence	266.863	336.19	1.25978
	nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09]	Low confidence	233.134	210.267	1.10875
60	fos-related antigen 2. [swissprot;acc:p15408]		202.793	182.961	1.10839
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08]	High confidence	266.864	336.184	1.25976
61	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670]			336.182	1.25975
	protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539]	Low confidence	202.792	182.974	1.10831
62	fos-related antigen 1 (fra-1). [swissprot;acc:p15407]		202.79	183.017	1.10804
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151]	High confidence	266.865	336.181	1.25974

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.