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

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Showing element 1 to 50 of 66312 in total

Filtered  : 1

Rank	description	Value Type	Network Comparison Type	Interaction Map	red	green	network_comparison
1	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976]	Measured	Subtracted	Low confidence	40899	32028.5	8870.5
		Ranked	Divided		16	32	2
		Squared	Subtracted		395912	242799	153113
	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	Ranked		High confidence	215	322	107
	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	Measured	Divided	Low confidence	2399.5	543.5	4.4149
		Ranked	Subtracted		223	330	107
		Squared	Divided		1362.75	69.9153	19.4914
		Rooted			48.9847	23.3131	2.10117
			Subtracted				25.6716
	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		High confidence	41482.5	33356.5	8126
	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	Ranked	Divided		10	24	2.4
		Squared	Subtracted		468498	322755	145743
	rad50-interacting protein 1. [refseq;acc:nm_021930]	Measured	Divided		450.5	2394.5	5.31521
		Squared			48.0356	1357.07	28.2513
		Rooted			21.225	48.9336	2.30547
			Subtracted				27.7086
2	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	Measured		Low confidence	21185	28492	7307
	bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090]	Squared			333556	475119	141563
	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	Measured	Divided		2399.5	543.5	4.4149
		Ranked	Subtracted		223	330	107
		Squared	Divided		1362.75	69.9153	19.4914
		Rooted			48.9847	23.3131	2.10117
			Subtracted				25.6716
	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	Measured		High confidence	41482.5	33356.5	8126
	hbs1-like. [refseq;acc:nm_006620]	Ranked			215	322	107
	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]		Divided	Low confidence	223	330	1.47982
	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]			High confidence	15	28	1.86667
		Squared	Subtracted		407289	263351	143938
	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	Measured	Divided		450.5	2394.5	5.31521
		Squared			48.0356	1357.07	28.2513
		Rooted			21.225	48.9336	2.30547
			Subtracted				27.7086
3	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	Ranked	Divided	Low confidence	223	330	1.47982
	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]	Measured			2399.5	543.5	4.4149
		Ranked	Subtracted		223	330	107
		Squared	Divided		1362.75	69.9153	19.4914
		Rooted			48.9847	23.3131	2.10117
			Subtracted				25.6716
	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	Ranked	Divided	High confidence	15	28	1.86667
		Squared	Subtracted		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]		Divided		2597.5	698.5	3.71868
		Squared			1596.92	115.48	13.8285
		Rooted			50.9657	26.4292	1.92839
			Subtracted				24.5365
	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	Measured		Low confidence	21185	28492	7307
	rad50-interacting protein 1. [refseq;acc:nm_021930]	Ranked		High confidence	337	232	105
	vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274]	Squared		Low confidence	333506	475045	141539
4	bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090]	Measured			36474.3	43509.4	7035.1
	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]	Ranked	Divided		223	330	1.47982

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.