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

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Showing element 1 to 50 of 3228 in total

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

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