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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

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

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.