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	green	network_comparison	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	green	network_comparison	red
1	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	Low confidence	543.5	4.4149	2399.5
	rad50-interacting protein 1. [refseq;acc:nm_021930]	High confidence	2394.5	5.31521	450.5
2	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	Low confidence	543.5	4.4149	2399.5
	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	High confidence	2394.5	5.31521	450.5
3	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]	Low confidence	543.5	4.4149	2399.5
	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	High confidence	698.5	3.71868	2597.5
4	hbs1-like. [refseq;acc:nm_006620]
	lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473]	Low confidence	543.5	4.4149	2399.5
5	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	High confidence	339.5	3.39764	1153.5
	oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3]	Low confidence	2113.5	2.86965	736.5
6	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	High confidence	339.5	3.39764	1153.5
	oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5]	Low confidence	2113.5	2.86965	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	339.5	3.39764	1153.5
8	db83 protein. [swissprot;acc:p57088]
	phosphatidylinositol-glycan biosynthesis, class f protein (pig-f). [swissprot;acc:q07326]	Low confidence	5058.5	1.54317	3278
9	n33 protein. [swissprot;acc:q13454]
	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	High confidence	1281.5	3.21581	398.5
10	implantation-associated protein. [refseq;acc:nm_032121]	Low confidence	5058.5	1.54317	3278
	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	High confidence	1281.5	3.21581	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	2950.5	1.53861	1917.64
12	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	High confidence	1281.5	3.21581	398.5
	gbp protein isoform a. [refseq;acc:nm_017870]	Low confidence	2954.24	1.5371	1921.96
13	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]	High confidence	1281.5	3.21581	398.5
	jumonji domain containing 1; zinc finger protein; testis-specific protein a. [refseq;acc:nm_018433]	Low confidence	2959.19	1.5351	1927.68
14	ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2]	High confidence	1281.5	3.21581	398.5
	trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [swissprot;acc:p35030]	Low confidence	2998.1	1.51983	1972.65
15	trypsin i precursor (ec 3.4.21.4) (cationic trypsinogen). [swissprot;acc:p07477]		3007.85	1.51612	1983.91
	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	High confidence	871	3.06659	2671
16	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	Low confidence	28492	1.34491	21185
	protein x 0004. [refseq;acc:nm_016301]	High confidence	871	3.06659	2671
17	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8]		1365	2.96739	460
	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	Low confidence	28492	1.34491	21185
18	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847]		7251	1.32027	5492.04
	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	High confidence	1865.5	2.75351	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	3915.4	1.29112	3032.56
	microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	High confidence	1865.5	2.75351	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	9368.87	1.29106	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]		3917.88	1.29072	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	1865.5	2.75351	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	3997.02	1.27828	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	1865.5	2.75351	677.5
23	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976]	Low confidence	32028.5	1.27696	40899
	gbp protein isoform a. [refseq;acc:nm_017870]	High confidence	1894.39	2.7072	699.76
24	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]	Low confidence	4577.5	1.24965	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	2108.52	2.21818	950.561
25	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262]		892.67	2.0534	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	4691.96	1.24627	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.