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

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Showing element 1 to 50 of 66312 in total

Filtered  : 1

Rank	description	Network Comparison Type	Value Type	Hugo	Interaction Map	red	green	network_comparison
1	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976]	Divided	Ranked	CPD	Low confidence	16	32	2
		Subtracted	Measured			40899	32028.5	8870.5
			Squared			395912	242799	153113
	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]		Ranked	HLX	High confidence	215	322	107
	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	Divided	Measured	LAMP1	Low confidence	2399.5	543.5	4.4149
			Squared			1362.75	69.9153	19.4914
			Rooted			48.9847	23.3131	2.10117
		Subtracted	Ranked			223	330	107
			Rooted			48.9847	23.3131	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	no value	High confidence	41482.5	33356.5	8126
	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	Divided	Ranked	UBAC1		10	24	2.4
		Subtracted	Squared			468498	322755	145743
	rad50-interacting protein 1. [refseq;acc:nm_021930]	Divided	Measured	RINT1		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	MRPS17	Low confidence	21185	28492	7307
	bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090]		Squared	BEST1		333556	475119	141563
	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	Divided	Measured	CDK4		2399.5	543.5	4.4149
			Squared			1362.75	69.9153	19.4914
			Rooted			48.9847	23.3131	2.10117
		Subtracted	Ranked			223	330	107
			Rooted			48.9847	23.3131	25.6716
	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]		Measured	PSCD1	High confidence	41482.5	33356.5	8126
	hbs1-like. [refseq;acc:nm_006620]		Ranked	HBS1L		215	322	107
	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	Divided		LAMP1	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]			no value	High confidence	15	28	1.86667
		Subtracted	Squared			407289	263351	143938
	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	Divided	Measured	RHOBTB2		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]	Divided	Ranked	CDK4	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	CDK6		2399.5	543.5	4.4149
			Squared			1362.75	69.9153	19.4914
			Rooted			48.9847	23.3131	2.10117
		Subtracted	Ranked			223	330	107
			Rooted			48.9847	23.3131	25.6716
	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	Divided	Ranked	PSCD1	High confidence	15	28	1.86667
		Subtracted	Squared			407289	263351	143938
	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]		Measured	PSCD2		41482.5	33356.5	8126
	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	Divided		HLX		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	SLC25A43	Low confidence	21185	28492	7307
	rad50-interacting protein 1. [refseq;acc:nm_021930]		Ranked	RINT1	High confidence	337	232	105
	vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274]		Squared	BEST4	Low confidence	333506	475045	141539
4	bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090]		Measured	BEST1		36474.3	43509.4	7035.1
	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]	Divided	Ranked	CDK6		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
- Hugo is the HGNC identifier if it exists
- 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.