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

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.