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	Network Comparison Type	Value Type	Interaction Map	Filtered	green	red	network_comparison

Results: HTML CSV LaTeX

Showing element 68 to 117 of 6456 in total

Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Network Comparison Type	green	red	network_comparison
34	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]	Divided	242.453	189.07	1.28235
35	guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775]	Subtracted	335.359	267.636	67.723
	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]	Divided	204.309	260.532	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]
	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]	Subtracted	254.434	320.927	66.493
37	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901]		333.165	266.716	66.449
	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	Divided	253	322	1.27273
38	guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0]	Subtracted	333.281	266.933	66.348
	microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	Divided	253	322	1.27273
39	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520]	Subtracted	334.483	268.565	65.918
	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]	Divided	253	322	1.27273
40	deltex 2. [refseq;acc:nm_020892]	Subtracted	267.393	333.144	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	253	322	1.27273
41	deltex homolog 1; hdx-1. [refseq;acc:nm_004416]	Subtracted	267.274	332.925	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	253	322	1.27273
42	proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100]		160.957	204.641	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	267.246	332.874	65.628
43	jun dimerization protein. [refseq;acc:nm_130469]	Divided	160.957	204.641	1.2714
	kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558]	Subtracted	267.246	332.874	65.628
44	fos-related antigen 2. [swissprot;acc:p15408]	Divided	161.046	204.641	1.2707
	kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559]	Subtracted	267.246	332.874	65.628
45	kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688]
	protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539]	Divided	161.051	204.641	1.27066
46	fos-related antigen 1 (fra-1). [swissprot;acc:p15407]		161.068	204.642	1.27053
	neuralized-like. [refseq;acc:nm_004210]	Subtracted	266.948	332.326	65.378
47	gbp protein isoform a. [refseq;acc:nm_017870]	Divided	256.492	325.586	1.26938
	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	Subtracted	290	350	60
48	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278]	Divided	83.0461	65.4586	1.26868
	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	Subtracted	290	350	60
49	beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121]	Divided	105	133	1.26667
	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]	Subtracted	290	350	60
50	beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]	Divided	105	133	1.26667
	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	Subtracted	290	350	60
51	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]
	spermatogenesis associated 6. [refseq;acc:nm_019073]	Divided	105	133	1.26667
52	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]
	ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2]	Subtracted	290	350	60
53	nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181]		259.004	318.982	59.978
	transcription factor jun-b. [swissprot;acc:p17275]	Divided	158.868	201.144	1.26611
54	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	Subtracted	245.247	185.678	59.569
	transcription factor jun-d. [swissprot;acc:p17535]	Divided	158.941	200.941	1.26425
55	glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216]	Subtracted	245.247	185.678	59.569
	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]	Divided	254.434	320.927	1.26134
56	glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737]	Subtracted	245.247	185.678	59.569
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262]	Divided	336.233	266.856	1.25998
57	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6]
	myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7]	Subtracted	245.247	185.678	59.569
58	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217]
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150]	Divided	336.191	266.863	1.25979
59	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798]		336.19		1.25978

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.