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

Results: HTML CSV LaTeX

Showing element 51 to 100 of 6456 in total

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

Rank	Network Comparison Type	description	red	network_comparison	green
26	Divided	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]	58	1.31818	44
	Subtracted	protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]	322	69	253
27	Divided	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	58	1.31818	44
	Subtracted	guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148]	267.136	68.941	336.077
28	Divided	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847]	201.949	1.31416	153.671
	Subtracted	guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992]	267.136	68.941	336.077
29	Divided	uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48]	187.458	1.29991	243.678
	Subtracted	guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086]	267.139	68.936	336.075
30	Divided	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]	187.457	1.29991	243.678
	Subtracted	guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087]	267.14	68.935	336.075
31	Divided	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]	187.458	1.2999	243.677
	Subtracted	guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488]	267.14	68.935	336.075
32	Divided	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]	187.462	1.29985	243.673
	Subtracted	guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899]	267.142	68.932	336.074
33	Divided	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]	188.688	1.28647	242.742
	Subtracted	guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898]	267.144	68.929	336.073
34	Divided	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]	189.07	1.28235	242.453
	Subtracted	guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754]	267.144	68.929	336.073
35	Divided	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]	260.532	1.27519	204.309
	Subtracted	guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775]	267.636	67.723	335.359
36	Divided	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]	260.532	1.27519	204.309
	Subtracted	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]	320.927	66.493	254.434
37	Divided	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	322	1.27273	253
	Subtracted	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901]	266.716	66.449	333.165
38	Divided	microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	322	1.27273	253
	Subtracted	guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0]	266.933	66.348	333.281
39	Divided	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]	322	1.27273	253
	Subtracted	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520]	268.565	65.918	334.483
40	Divided	ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485]	322	1.27273	253
	Subtracted	deltex 2. [refseq;acc:nm_020892]	333.144	65.751	267.393
41	Divided	protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]	322	1.27273	253
	Subtracted	deltex homolog 1; hdx-1. [refseq;acc:nm_004416]	332.925	65.651	267.274
42	Divided	proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100]	204.641	1.2714	160.957
	Subtracted	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]	332.874	65.628	267.246
43	Divided	jun dimerization protein. [refseq;acc:nm_130469]	204.641	1.2714	160.957
	Subtracted	kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558]	332.874	65.628	267.246
44	Divided	fos-related antigen 2. [swissprot;acc:p15408]	204.641	1.2707	161.046
	Subtracted	kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559]	332.874	65.628	267.246
45	Divided	protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539]	204.641	1.27066	161.051
	Subtracted	kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688]	332.874	65.628	267.246
46	Divided	fos-related antigen 1 (fra-1). [swissprot;acc:p15407]	204.642	1.27053	161.068
	Subtracted	neuralized-like. [refseq;acc:nm_004210]	332.326	65.378	266.948
47	Divided	gbp protein isoform a. [refseq;acc:nm_017870]	325.586	1.26938	256.492
	Subtracted	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	350	60	290
48	Divided	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278]	65.4586	1.26868	83.0461
	Subtracted	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	350	60	290
49	Divided	beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121]	133	1.26667	105
	Subtracted	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]	350	60	290
50	Divided	beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]	133	1.26667	105
	Subtracted	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	350	60	290

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.