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

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Showing element 1 to 50 of 8289 in total

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

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

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.