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

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Showing element 1 to 50 of 8289 in total

Value Type  : Ranked
Filtered  : 1
Network Comparison Type  : Divided

Rank	description	Interaction Map	network_comparison	green	red
1	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976]	Low confidence	2	32	16
	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	High confidence	2.4	24	10
2	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	Low confidence	1.47982	330	223
	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]	High confidence	1.86667	28	15
3	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	Low confidence	1.47982	330	223
	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	High confidence	1.86667	28	15
4	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]	Low confidence	1.47982	330	223
	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	High confidence	1.86667	28	15
5	cytohesin 4. [swissprot;acc:q9uia0]
	lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473]	Low confidence	1.47982	330	223
6	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	High confidence	1.86667	28	15
	oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3]	Low confidence	1.325	240	318
7	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	High confidence	1.49767	322	215
	oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5]	Low confidence	1.325	240	318
8	hbs1-like. [refseq;acc:nm_006620]	High confidence	1.49767	322	215
	oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2]	Low confidence	1.325	240	318
9	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]		1.31818	44	58
	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	High confidence	1.45755	309	212
10	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	Low confidence	1.31818	44	58
	protein x 0004. [refseq;acc:nm_016301]	High confidence	1.45755	309	212
11	bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090]	Low confidence	1.30966	28.4944	37.318
	rad50-interacting protein 1. [refseq;acc:nm_021930]	High confidence	1.45259	232	337
12	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]
	vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274]	Low confidence	1.30933	28.5242	37.3475
13	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]		1.30207	29.1831	37.9984
	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	High confidence	1.3585	212.554	288.754
14	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]		1.32952	75.3531	56.6768
	vitelliform macular dystrophy 2-like protein 1. [refseq;acc:nm_017682]	Low confidence	1.30207	29.1831	37.9984
15	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8]	High confidence	1.32914	75.3948	56.7244
	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	Low confidence	1.26035	202.362	255.046
16	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492]	High confidence	1.32913	75.3954	56.7252
	thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652]	Low confidence	1.2355	247.246	305.472
17	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	High confidence	1.32866	75.447	56.7841
	gbp protein isoform a. [refseq;acc:nm_017870]	Low confidence	1.23537	247.213	305.399
18	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	High confidence	1.32082	245.247	185.678
	jumonji domain containing 1; zinc finger protein; testis-specific protein a. [refseq;acc:nm_018433]	Low confidence	1.2352	247.169	305.303
19	glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216]	High confidence	1.32082	245.247	185.678
	trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [swissprot;acc:p35030]	Low confidence	1.23387	246.824	304.548
20	glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737]	High confidence	1.32082	245.247	185.678
	trypsin i precursor (ec 3.4.21.4) (cationic trypsinogen). [swissprot;acc:p07477]	Low confidence	1.23354	246.737	304.359
21	myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7]	High confidence	1.32082	245.247	185.678
	phosphatidylinositol-glycan biosynthesis, class f protein (pig-f). [swissprot;acc:q07326]	Low confidence	1.21472	163	198
22	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217]	High confidence	1.32082	245.247	185.678
	n33 protein. [swissprot;acc:q13454]	Low confidence	1.21472	163	198
23	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	High confidence	1.31818	44	58
	implantation-associated protein. [refseq;acc:nm_032121]	Low confidence	1.21472	163	198
24	histidine triad nucleotide-binding protein 1 (adenosine 5'- monophosphoramidase) (protein kinase c inhibitor 1) (protein kinase c- interacting protein 1) (pkci-1). [swissprot;acc:p49773]		1.21355	228.509	188.298
	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]	High confidence	1.31818	44	58
25	25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [swissprot;acc:o15528]	Low confidence	1.20094	238.476	286.396
	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]	High confidence	1.31818	44	58

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.