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

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Showing element 1 to 50 of 33156 in total

Network Comparison Type  : Divided
Filtered  : 1

Rank	Interaction Map	description	Value Type	red	network_comparison	green
1	High confidence	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	Ranked	10	2.4	24
		rad50-interacting protein 1. [refseq;acc:nm_021930]	Measured	450.5	5.31521	2394.5
			Squared	48.0356	28.2513	1357.07
			Rooted	21.225	2.30547	48.9336
	Low confidence	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976]	Ranked	16	2	32
		lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	Measured	2399.5	4.4149	543.5
			Squared	1362.75	19.4914	69.9153
			Rooted	48.9847	2.10117	23.3131
2	High confidence	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]	Ranked	15	1.86667	28
		rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	Measured	450.5	5.31521	2394.5
			Squared	48.0356	28.2513	1357.07
			Rooted	21.225	2.30547	48.9336
	Low confidence	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	Measured	2399.5	4.4149	543.5
			Squared	1362.75	19.4914	69.9153
			Rooted	48.9847	2.10117	23.3131
		lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	Ranked	223	1.47982	330
3	High confidence	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]		15	1.86667	28
		homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	Measured	2597.5	3.71868	698.5
			Squared	1596.92	13.8285	115.48
			Rooted	50.9657	1.92839	26.4292
	Low confidence	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	Ranked	223	1.47982	330
		cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]	Measured	2399.5	4.4149	543.5
			Squared	1362.75	19.4914	69.9153
			Rooted	48.9847	2.10117	23.3131
4	High confidence	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	Ranked	15	1.86667	28
		hbs1-like. [refseq;acc:nm_006620]	Measured	2597.5	3.71868	698.5
			Squared	1596.92	13.8285	115.48
			Rooted	50.9657	1.92839	26.4292
	Low confidence	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]	Ranked	223	1.47982	330
		lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473]	Measured	2399.5	4.4149	543.5
			Squared	1362.75	19.4914	69.9153
			Rooted	48.9847	2.10117	23.3131
5	High confidence	cytohesin 4. [swissprot;acc:q9uia0]	Ranked	15	1.86667	28
		junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	Measured	1153.5	3.39764	339.5
			Squared	314.926	11.544	27.2805
			Rooted	33.9632	1.84327	18.4255
	Low confidence	lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473]	Ranked	223	1.47982	330
		oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3]	Measured	736.5	2.86965	2113.5
			Squared	128.386	8.23493	1057.25
			Rooted	27.1385	1.69401	45.9728
6	High confidence	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	Ranked	15	1.86667	28
		junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	Measured	1153.5	3.39764	339.5
			Squared	314.926	11.544	27.2805
			Rooted	33.9632	1.84327	18.4255
	Low confidence	oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5]	Measured	736.5	2.86965	2113.5
			Squared	128.386	8.23493	1057.25
			Rooted	27.1385	1.69401	45.9728
		oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3]	Ranked	318	1.325	240
7	High confidence	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]		215	1.49767	322
		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]	Measured	1153.5	3.39764	339.5

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.