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 158 to 207 of 16578 in total

Value Type  : Ranked
Filtered  : 1

Rank	description	Network Comparison Type	Interaction Map	red	green	network_comparison
40	deltex 2. [refseq;acc:nm_020892]	Subtracted	High confidence	333.144	267.393	65.751
	ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485]	Divided		322	253	1.27273
	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
	deltex homolog 1; hdx-1. [refseq;acc:nm_004416]	Subtracted	High confidence	332.925	267.274	65.651
	protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]	Divided		322	253	1.27273
	putative rna-binding protein 7 (rna binding motif protein 7). [swissprot;acc:q9y580]	Subtracted	Low confidence	265.688	239.902	25.786
42	glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417]	Divided		227.371	200.532	1.13384
	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	Subtracted		242.742	217.217	25.525
	proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100]	Divided	High confidence	204.641	160.957	1.2714
	t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492]	Subtracted		332.874	267.246	65.628
43	jun dimerization protein. [refseq;acc:nm_130469]	Divided		204.641	160.957	1.2714
	kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558]	Subtracted		332.874	267.246	65.628
	microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]		Low confidence	242.742	217.217	25.525
	regulator of g-protein signaling 12 (rgs12). [swissprot;acc:o14924]	Divided		247.768	219.841	1.12703
44	fos-related antigen 2. [swissprot;acc:p15408]		High confidence	204.641	161.046	1.2707
	kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559]	Subtracted		332.874	267.246	65.628
	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	Divided	Low confidence	242.742	217.217	1.11751
	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]	Subtracted				25.525
45	ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485]
	kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688]		High confidence	332.874	267.246	65.628
	microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	Divided	Low confidence	242.742	217.217	1.11751
	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
	neuralized-like. [refseq;acc:nm_004210]	Subtracted		332.326	266.948	65.378
	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	25.525
	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]	Divided				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
	testis-specific protein tex28. [swissprot;acc:o15482]	Subtracted	Low confidence	259.517	235.017	24.5
	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]		High confidence	350	290	60
48	27 kda golgi snare protein (golgi snap receptor complex member 2) (membrin). [swissprot;acc:o14653]		Low confidence	259.517	235.017	24.5
	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278]	Divided	High confidence	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
	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	Subtracted	High confidence	350	290	60
49	beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121]	Divided		133	105	1.26667
	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]	Subtracted		350	290	60
	t-box transcription factor tbx19 (t-box protein 19). [swissprot;acc:o60806]	Divided	Low confidence	225.438	202.569	1.11289
		Subtracted				22.869
50	beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]	Divided	High confidence	133	105	1.26667
	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	Subtracted		350	290	60
	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	Divided	Low confidence	234.802	260.98	1.11149
	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]	Subtracted		233.134	210.267	22.867
51	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]		High confidence	350	290	60
	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	Divided	Low confidence	234.802	260.98	1.11149
	nipsnap2 protein (glioblastoma amplified sequence). [swissprot;acc:o75323]	Subtracted		249.709	226.944	22.765
	spermatogenesis associated 6. [refseq;acc:nm_019073]	Divided	High confidence	133	105	1.26667
52	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]
	nipsnap1 protein. [swissprot;acc:q9bpw8]	Subtracted	Low confidence	249.584	226.86	22.724
	ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2]		High confidence	350	290	60

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.