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

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Showing element 1 to 50 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

Rank	Value Type	description	Network Comparison Type	green	red	network_comparison
1	Measured	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]	Subtracted	33356.5	41482.5	8126
		rad50-interacting protein 1. [refseq;acc:nm_021930]	Divided	2394.5	450.5	5.31521
	Ranked	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	Subtracted	322	215	107
		putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	Divided	24	10	2.4
	Squared		Subtracted	322755	468498	145743
		rad50-interacting protein 1. [refseq;acc:nm_021930]	Divided	1357.07	48.0356	28.2513
	Rooted			48.9336	21.225	2.30547
			Subtracted			27.7086
2	Measured	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]		33356.5	41482.5	8126
		rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	Divided	2394.5	450.5	5.31521
	Ranked	hbs1-like. [refseq;acc:nm_006620]	Subtracted	322	215	107
		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]	Divided	28	15	1.86667
	Squared		Subtracted	263351	407289	143938
		rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	Divided	1357.07	48.0356	28.2513
	Rooted			48.9336	21.225	2.30547
			Subtracted			27.7086
3	Measured	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]		33356.5	41482.5	8126
		homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	Divided	698.5	2597.5	3.71868
	Ranked	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]		28	15	1.86667
		rad50-interacting protein 1. [refseq;acc:nm_021930]	Subtracted	232	337	105
	Squared	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]		263351	407289	143938
		homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	Divided	115.48	1596.92	13.8285
	Rooted			26.4292	50.9657	1.92839
			Subtracted			24.5365
4	Measured	cytohesin 4. [swissprot;acc:q9uia0]		33356.5	41482.5	8126
		hbs1-like. [refseq;acc:nm_006620]	Divided	698.5	2597.5	3.71868
	Ranked	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]		28	15	1.86667
		rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	Subtracted	232	337	105
	Squared	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]		263351	407289	143938
		hbs1-like. [refseq;acc:nm_006620]	Divided	115.48	1596.92	13.8285
	Rooted			26.4292	50.9657	1.92839
			Subtracted			24.5365
5	Measured	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]		33356.5	41482.5	8126
		junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	Divided	339.5	1153.5	3.39764
	Ranked	cytohesin 4. [swissprot;acc:q9uia0]		28	15	1.86667
		xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	Subtracted	309	212	97
	Squared	cytohesin 4. [swissprot;acc:q9uia0]		263351	407289	143938
		junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	Divided	27.2805	314.926	11.544
	Rooted	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	Subtracted	168.796	145.551	23.245
		junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	Divided	18.4255	33.9632	1.84327
6	Measured	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]		339.5	1153.5	3.39764
		putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	Subtracted	36927.5	44490.5	7563
	Ranked	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	Divided	28	15	1.86667
		protein x 0004. [refseq;acc:nm_016301]	Subtracted	309	212	97
	Squared	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]		263351	407289	143938
		junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	Divided	27.2805	314.926	11.544
	Rooted			18.4255	33.9632	1.84327
		pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]	Subtracted	168.796	145.551	23.245
7	Measured	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]		28492	21185	7307
		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]	Divided	339.5	1153.5	3.39764

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.