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	Network Comparison Type	Value Type	Interaction Map	Filtered	green	red	network_comparison

Results: HTML CSV LaTeX

Showing element 1 to 50 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

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

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.