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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

Rank	description	red	Value Type	Network Comparison Type	network_comparison	green
1	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	215	Ranked	Subtracted	107	322
	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	Measured		8126	33356.5
	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	10	Ranked	Divided	2.4	24
		468498	Squared	Subtracted	145743	322755
	rad50-interacting protein 1. [refseq;acc:nm_021930]	21.225	Rooted	Divided	2.30547	48.9336
				Subtracted	27.7086
		48.0356	Squared	Divided	28.2513	1357.07
		450.5	Measured		5.31521	2394.5
2	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	41482.5		Subtracted	8126	33356.5
	hbs1-like. [refseq;acc:nm_006620]	215	Ranked		107	322
	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		Divided	1.86667	28
		407289	Squared	Subtracted	143938	263351
	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	21.225	Rooted	Divided	2.30547	48.9336
				Subtracted	27.7086
		48.0356	Squared	Divided	28.2513	1357.07
		450.5	Measured		5.31521	2394.5
3	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	15	Ranked		1.86667	28
		407289	Squared	Subtracted	143938	263351
	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	41482.5	Measured		8126	33356.5
	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	50.9657	Rooted	Divided	1.92839	26.4292
				Subtracted	24.5365
		1596.92	Squared	Divided	13.8285	115.48
		2597.5	Measured		3.71868	698.5
	rad50-interacting protein 1. [refseq;acc:nm_021930]	337	Ranked	Subtracted	105	232
4	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	15		Divided	1.86667	28
		407289	Squared	Subtracted	143938	263351
	cytohesin 4. [swissprot;acc:q9uia0]	41482.5	Measured		8126	33356.5
	hbs1-like. [refseq;acc:nm_006620]	50.9657	Rooted	Divided	1.92839	26.4292
				Subtracted	24.5365
		1596.92	Squared	Divided	13.8285	115.48
		2597.5	Measured		3.71868	698.5
	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	337	Ranked	Subtracted	105	232
5	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	145.551	Rooted		23.245	168.796
	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	41482.5	Measured		8126	33356.5
	cytohesin 4. [swissprot;acc:q9uia0]	15	Ranked	Divided	1.86667	28
		407289	Squared	Subtracted	143938	263351
	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	33.9632	Rooted	Divided	1.84327	18.4255
		314.926	Squared		11.544	27.2805
		1153.5	Measured		3.39764	339.5
	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	212	Ranked	Subtracted	97	309
6	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	15		Divided	1.86667	28
		407289	Squared	Subtracted	143938	263351
	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	33.9632	Rooted	Divided	1.84327	18.4255
		314.926	Squared		11.544	27.2805
		1153.5	Measured		3.39764	339.5
	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]	145.551	Rooted	Subtracted	23.245	168.796
	protein x 0004. [refseq;acc:nm_016301]	212	Ranked		97	309
	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	44490.5	Measured		7563	36927.5
7	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	21185			7307	28492
	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	215	Ranked	Divided	1.49767	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.