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

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Showing element 1 to 50 of 33156 in total

Network Comparison Type  : Divided
Filtered  : 1

Rank	Value Type	description	network_comparison	green	Interaction Map	red
1	Measured	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	4.4149	543.5	Low confidence	2399.5
		rad50-interacting protein 1. [refseq;acc:nm_021930]	5.31521	2394.5	High confidence	450.5
	Ranked	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976]	2	32	Low confidence	16
		putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	2.4	24	High confidence	10
	Squared	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	19.4914	69.9153	Low confidence	1362.75
		rad50-interacting protein 1. [refseq;acc:nm_021930]	28.2513	1357.07	High confidence	48.0356
	Rooted	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	2.10117	23.3131	Low confidence	48.9847
		rad50-interacting protein 1. [refseq;acc:nm_021930]	2.30547	48.9336	High confidence	21.225
2	Measured	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	4.4149	543.5	Low confidence	2399.5
		rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	5.31521	2394.5	High confidence	450.5
	Ranked	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	1.47982	330	Low confidence	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]	1.86667	28	High confidence	15
	Squared	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	19.4914	69.9153	Low confidence	1362.75
		rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	28.2513	1357.07	High confidence	48.0356
	Rooted	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	2.10117	23.3131	Low confidence	48.9847
		rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	2.30547	48.9336	High confidence	21.225
3	Measured	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]	4.4149	543.5	Low confidence	2399.5
		homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	3.71868	698.5	High confidence	2597.5
	Ranked	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	1.47982	330	Low confidence	223
		cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	1.86667	28	High confidence	15
	Squared	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]	19.4914	69.9153	Low confidence	1362.75
		homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	13.8285	115.48	High confidence	1596.92
	Rooted	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]	2.10117	23.3131	Low confidence	48.9847
		homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	1.92839	26.4292	High confidence	50.9657
4	Measured	hbs1-like. [refseq;acc:nm_006620]	3.71868	698.5		2597.5
		lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473]	4.4149	543.5	Low confidence	2399.5
	Ranked	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]	1.47982	330		223
		cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	1.86667	28	High confidence	15
	Squared	hbs1-like. [refseq;acc:nm_006620]	13.8285	115.48		1596.92
		lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473]	19.4914	69.9153	Low confidence	1362.75
	Rooted	hbs1-like. [refseq;acc:nm_006620]	1.92839	26.4292	High confidence	50.9657
		lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473]	2.10117	23.3131	Low confidence	48.9847
5	Measured	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	3.39764	339.5	High confidence	1153.5
		oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3]	2.86965	2113.5	Low confidence	736.5
	Ranked	cytohesin 4. [swissprot;acc:q9uia0]	1.86667	28	High confidence	15
		lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473]	1.47982	330	Low confidence	223
	Squared	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	11.544	27.2805	High confidence	314.926
		oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3]	8.23493	1057.25	Low confidence	128.386
	Rooted	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	1.84327	18.4255	High confidence	33.9632
		oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3]	1.69401	45.9728	Low confidence	27.1385
6	Measured	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	3.39764	339.5	High confidence	1153.5
		oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5]	2.86965	2113.5	Low confidence	736.5
	Ranked	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	1.86667	28	High confidence	15
		oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3]	1.325	240	Low confidence	318
	Squared	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	11.544	27.2805	High confidence	314.926
		oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5]	8.23493	1057.25	Low confidence	128.386
	Rooted	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	1.84327	18.4255	High confidence	33.9632
		oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5]	1.69401	45.9728	Low confidence	27.1385
7	Measured	oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2]	2.86965	2113.5		736.5
		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]	3.39764	339.5	High confidence	1153.5

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.