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

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Showing element 1 to 50 of 25824 in total

Filtered  : 1
Interaction Map  : High confidence

Rank	Network Comparison Type	description	Value Type	green	network_comparison	red
1	Divided	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	Ranked	24	2.4	10
		rad50-interacting protein 1. [refseq;acc:nm_021930]	Measured	2394.5	5.31521	450.5
			Squared	1357.07	28.2513	48.0356
			Rooted	48.9336	2.30547	21.225
	Subtracted	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	Ranked	322	107	215
		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]	Measured	33356.5	8126	41482.5
		putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	Squared	322755	145743	468498
		rad50-interacting protein 1. [refseq;acc:nm_021930]	Rooted	48.9336	27.7086	21.225
2	Divided	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]	Ranked	28	1.86667	15
		rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	Measured	2394.5	5.31521	450.5
			Squared	1357.07	28.2513	48.0356
			Rooted	48.9336	2.30547	21.225
	Subtracted	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	Measured	33356.5	8126	41482.5
		hbs1-like. [refseq;acc:nm_006620]	Ranked	322	107	215
		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]	Squared	263351	143938	407289
		rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	Rooted	48.9336	27.7086	21.225
3	Divided	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	Ranked	28	1.86667	15
		homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	Measured	698.5	3.71868	2597.5
			Squared	115.48	13.8285	1596.92
			Rooted	26.4292	1.92839	50.9657
	Subtracted	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	Squared	263351	143938	407289
		cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	Measured	33356.5	8126	41482.5
		homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	Rooted	26.4292	24.5365	50.9657
		rad50-interacting protein 1. [refseq;acc:nm_021930]	Ranked	232	105	337
4	Divided	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]		28	1.86667	15
		hbs1-like. [refseq;acc:nm_006620]	Measured	698.5	3.71868	2597.5
			Squared	115.48	13.8285	1596.92
			Rooted	26.4292	1.92839	50.9657
	Subtracted	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	Squared	263351	143938	407289
		cytohesin 4. [swissprot;acc:q9uia0]	Measured	33356.5	8126	41482.5
		hbs1-like. [refseq;acc:nm_006620]	Rooted	26.4292	24.5365	50.9657
		rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	Ranked	232	105	337
5	Divided	cytohesin 4. [swissprot;acc:q9uia0]		28	1.86667	15
		junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	Measured	339.5	3.39764	1153.5
			Squared	27.2805	11.544	314.926
			Rooted	18.4255	1.84327	33.9632
	Subtracted	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]		168.796	23.245	145.551
		cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	Measured	33356.5	8126	41482.5
		cytohesin 4. [swissprot;acc:q9uia0]	Squared	263351	143938	407289
		xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	Ranked	309	97	212
6	Divided	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]		28	1.86667	15
		junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	Measured	339.5	3.39764	1153.5
			Squared	27.2805	11.544	314.926
			Rooted	18.4255	1.84327	33.9632
	Subtracted	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	Squared	263351	143938	407289
		pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]	Rooted	168.796	23.245	145.551
		protein x 0004. [refseq;acc:nm_016301]	Ranked	309	97	212
		putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	Measured	36927.5	7563	44490.5
7	Divided	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	Ranked	322	1.49767	215
		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]	Measured	339.5	3.39764	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.