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

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Showing element 1 to 50 of 66312 in total

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

Rank	description	Interaction Map	network_comparison	green	red
1	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	Low confidence	4.4149	543.5	2399.5
	rad50-interacting protein 1. [refseq;acc:nm_021930]	High confidence	5.31521	2394.5	450.5
2	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	Low confidence	4.4149	543.5	2399.5
	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	High confidence	5.31521	2394.5	450.5
3	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]	Low confidence	4.4149	543.5	2399.5
	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	High confidence	3.71868	698.5	2597.5
4	hbs1-like. [refseq;acc:nm_006620]
	lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473]	Low confidence	4.4149	543.5	2399.5
5	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	High confidence	3.39764	339.5	1153.5
	oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3]	Low confidence	2.86965	2113.5	736.5
6	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	High confidence	3.39764	339.5	1153.5
	oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5]	Low confidence	2.86965	2113.5	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]	High confidence	3.39764	339.5	1153.5
8	db83 protein. [swissprot;acc:p57088]
	phosphatidylinositol-glycan biosynthesis, class f protein (pig-f). [swissprot;acc:q07326]	Low confidence	1.54317	5058.5	3278
9	n33 protein. [swissprot;acc:q13454]
	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	High confidence	3.21581	1281.5	398.5
10	implantation-associated protein. [refseq;acc:nm_032121]	Low confidence	1.54317	5058.5	3278
	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	High confidence	3.21581	1281.5	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]	Low confidence	1.53861	2950.5	1917.64
12	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	High confidence	3.21581	1281.5	398.5
	gbp protein isoform a. [refseq;acc:nm_017870]	Low confidence	1.5371	2954.24	1921.96
13	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]	High confidence	3.21581	1281.5	398.5
	jumonji domain containing 1; zinc finger protein; testis-specific protein a. [refseq;acc:nm_018433]	Low confidence	1.5351	2959.19	1927.68
14	ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2]	High confidence	3.21581	1281.5	398.5
	trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [swissprot;acc:p35030]	Low confidence	1.51983	2998.1	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]	High confidence	3.06659	871	2671
16	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	Low confidence	1.34491	28492	21185
	protein x 0004. [refseq;acc:nm_016301]	High confidence	3.06659	871	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]	Low confidence	1.34491	28492	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]	High confidence	2.75351	1865.5	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]	Low confidence	1.29112	3915.4	3032.56
	microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	High confidence	2.75351	1865.5	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]	Low confidence	1.29106	9368.87	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]	High confidence	2.75351	1865.5	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]	Low confidence	1.27828	3997.02	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]	High confidence	2.75351	1865.5	677.5
23	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976]	Low confidence	1.27696	32028.5	40899
	gbp protein isoform a. [refseq;acc:nm_017870]	High confidence	2.7072	1894.39	699.76
24	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]	Low confidence	1.24965	4577.5	5720.25
	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]	High confidence	2.21818	2108.52	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]	Low confidence	1.24627	4691.96	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.