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

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Showing element 1 to 50 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

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