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

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

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.