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

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Showing element 1 to 50 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

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

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.