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

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Showing element 1 to 50 of 3228 in total

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

Rank	red	network_comparison	green	description
1	10	2.4	24	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]
2	15	1.86667	28	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]
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	215	1.49767	322	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]
8				hbs1-like. [refseq;acc:nm_006620]
9	212	1.45755	309	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]
10				protein x 0004. [refseq;acc:nm_016301]
11	337	1.45259	232	rad50-interacting protein 1. [refseq;acc:nm_021930]
12				rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]
13	288.754	1.3585	212.554	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]
14	56.6768	1.32952	75.3531	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]
15	56.7244	1.32914	75.3948	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8]
16	56.7252	1.32913	75.3954	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492]
17	56.7841	1.32866	75.447	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]
18	185.678	1.32082	245.247	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]
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	58	1.31818	44	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]
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	201.949	1.31416	153.671	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847]
29	187.458	1.29991	243.678	uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48]
30	187.457			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]
31	187.458	1.2999	243.677	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]
32	187.462	1.29985	243.673	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]
33	188.688	1.28647	242.742	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]
34	189.07	1.28235	242.453	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]
35	260.532	1.27519	204.309	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]
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	322	1.27273	253	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]
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	204.641	1.2714	160.957	proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100]
43				jun dimerization protein. [refseq;acc:nm_130469]
44		1.2707	161.046	fos-related antigen 2. [swissprot;acc:p15408]
45		1.27066	161.051	protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539]
46	204.642	1.27053	161.068	fos-related antigen 1 (fra-1). [swissprot;acc:p15407]
47	325.586	1.26938	256.492	gbp protein isoform a. [refseq;acc:nm_017870]
48	65.4586	1.26868	83.0461	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278]
49	133	1.26667	105	beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121]
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.