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	Value Type	Network Comparison Type	Interaction Map	Filtered	red	green	network_comparison

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Showing element 1 to 50 of 33156 in total

Network Comparison Type  : Divided
Filtered  : 1

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

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.