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	Interaction Map	Value Type	Network Comparison Type	red	network_comparison	Filtered	green

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Showing element 1 to 50 of 33156 in total

Network Comparison Type  : Divided
Filtered  : 1

Rank	description	Interaction Map	Value Type	red	network_comparison	green
1	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976]	Low confidence	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
	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	High confidence	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
2	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	Low confidence	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
	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		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
3	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	Low confidence	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
	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	High confidence	Ranked	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
4	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]	Low confidence	Ranked	223	1.47982	330
	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	High confidence		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
	lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473]	Low confidence	Measured	2399.5	4.4149	543.5
			Squared	1362.75	19.4914	69.9153
			Rooted	48.9847	2.10117	23.3131
5	cytohesin 4. [swissprot;acc:q9uia0]	High confidence	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
	lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473]	Low confidence	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	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	High confidence	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
	oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5]	Low confidence	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	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	High confidence		215	1.49767	322
	oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5]	Low confidence		318	1.325	240

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.