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	description	Network Comparison Type	Interaction Map	Filtered	red	network_comparison	green

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Showing element 1 to 50 of 3228 in total

Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1

Rank	description	red	network_comparison	green
1	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	10	2.4	24
2	mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476]	15	1.86667	28
3	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]
4	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]
5	cytohesin 4. [swissprot;acc:q9uia0]
6	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]
7	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	215	1.49767	322
8	hbs1-like. [refseq;acc:nm_006620]
9	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	212	1.45755	309
10	protein x 0004. [refseq;acc:nm_016301]
11	rad50-interacting protein 1. [refseq;acc:nm_021930]	337	1.45259	232
12	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]
13	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	288.754	1.3585	212.554
14	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	56.6768	1.32952	75.3531
15	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8]	56.7244	1.32914	75.3948
16	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492]	56.7252	1.32913	75.3954
17	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	56.7841	1.32866	75.447
18	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	185.678	1.32082	245.247
19	glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216]
20	glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737]
21	myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7]
22	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217]
23	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	58	1.31818	44
24	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]
25	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]
26	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]
27	mitochondrial solute carrier protein. [refseq;acc:nm_145305]
28	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847]	201.949	1.31416	153.671
29	uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48]	187.458	1.29991	243.678
30	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
31	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
32	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
33	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
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]	189.07	1.28235	242.453
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]	260.532	1.27519	204.309
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]
37	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	322	1.27273	253
38	microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]
39	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]
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]
41	protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]
42	proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100]	204.641	1.2714	160.957
43	jun dimerization protein. [refseq;acc:nm_130469]
44	fos-related antigen 2. [swissprot;acc:p15408]		1.2707	161.046
45	protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539]		1.27066	161.051
46	fos-related antigen 1 (fra-1). [swissprot;acc:p15407]	204.642	1.27053	161.068
47	gbp protein isoform a. [refseq;acc:nm_017870]	325.586	1.26938	256.492
48	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278]	65.4586	1.26868	83.0461
49	beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121]	133	1.26667	105
50	beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]

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.