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

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Showing element 1 to 50 of 33156 in total

Filtered  : 1
Network Comparison Type  : Divided

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

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.