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	Filtered	green	Interaction Map	red	network_comparison

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Showing element 1 to 50 of 66312 in total

Filtered  : 1

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