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

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Showing element 1 to 50 of 33156 in total

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

Rank	description	network_comparison	green	Interaction Map	red
1	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	4.4149	543.5	Low confidence	2399.5
	rad50-interacting protein 1. [refseq;acc:nm_021930]	5.31521	2394.5	High confidence	450.5
2	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	4.4149	543.5	Low confidence	2399.5
	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	5.31521	2394.5	High confidence	450.5
3	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]	4.4149	543.5	Low confidence	2399.5
	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	3.71868	698.5	High confidence	2597.5
4	hbs1-like. [refseq;acc:nm_006620]
	lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473]	4.4149	543.5	Low confidence	2399.5
5	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	3.39764	339.5	High confidence	1153.5
	oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3]	2.86965	2113.5	Low confidence	736.5
6	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	3.39764	339.5	High confidence	1153.5
	oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5]	2.86965	2113.5	Low confidence	736.5
7	oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2]
	sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906]	3.39764	339.5	High confidence	1153.5
8	db83 protein. [swissprot;acc:p57088]
	phosphatidylinositol-glycan biosynthesis, class f protein (pig-f). [swissprot;acc:q07326]	1.54317	5058.5	Low confidence	3278
9	n33 protein. [swissprot;acc:q13454]
	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	3.21581	1281.5	High confidence	398.5
10	implantation-associated protein. [refseq;acc:nm_032121]	1.54317	5058.5	Low confidence	3278
	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	3.21581	1281.5	High confidence	398.5
11	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]
	thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652]	1.53861	2950.5	Low confidence	1917.64
12	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	3.21581	1281.5	High confidence	398.5
	gbp protein isoform a. [refseq;acc:nm_017870]	1.5371	2954.24	Low confidence	1921.96
13	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]	3.21581	1281.5	High confidence	398.5
	jumonji domain containing 1; zinc finger protein; testis-specific protein a. [refseq;acc:nm_018433]	1.5351	2959.19	Low confidence	1927.68
14	ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2]	3.21581	1281.5	High confidence	398.5
	trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [swissprot;acc:p35030]	1.51983	2998.1	Low confidence	1972.65
15	trypsin i precursor (ec 3.4.21.4) (cationic trypsinogen). [swissprot;acc:p07477]	1.51612	3007.85		1983.91
	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	3.06659	871	High confidence	2671
16	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	1.34491	28492	Low confidence	21185
	protein x 0004. [refseq;acc:nm_016301]	3.06659	871	High confidence	2671
17	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8]	2.96739	1365		460
	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	1.34491	28492	Low confidence	21185
18	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847]	1.32027	7251		5492.04
	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	2.75351	1865.5	High confidence	677.5
19	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]	1.29112	3915.4	Low confidence	3032.56
	microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	2.75351	1865.5	High confidence	677.5
20	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]
	retinoblastoma-associated factor 600. [refseq;acc:nm_020765]	1.29106	9368.87	Low confidence	7256.71
21	cytochrome p450 27, mitochondrial precursor (ec 1.14.-.-) (cytochrome p-450c27/25) (sterol 26-hydroxylase) (sterol 27-hydroxylase) (vitamin d(3) 25-hydroxylase) (5-beta-cholestane-3-alpha,7-alpha,12-alpha-triol 27-hydroxylase). [swissprot;acc:q02318]	1.29072	3917.88		3035.43
	ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485]	2.75351	1865.5	High confidence	677.5
22	cytochrome p450 24a1, mitochondrial precursor (ec 1.14.-.-) (p450- cc24) (vitamin d(3) 24-hydroxylase) (1,25-dihydroxyvitamin d(3) 24- hydroxylase) (24-ohase). [swissprot;acc:q07973]	1.27828	3997.02	Low confidence	3126.88
	protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]	2.75351	1865.5	High confidence	677.5
23	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976]	1.27696	32028.5	Low confidence	40899
	gbp protein isoform a. [refseq;acc:nm_017870]	2.7072	1894.39	High confidence	699.76
24	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]	1.24965	4577.5	Low confidence	5720.25
	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]	2.21818	2108.52	High confidence	950.561
25	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262]	2.0534	892.67		1833.01
	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]	1.24627	4691.96	Low confidence	5847.46

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.