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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.

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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

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