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

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.