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

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Showing element 1 to 50 of 66312 in total

Filtered  : 1

Rank	Hugo	Value Type	description	Network Comparison Type	Interaction Map	red	green	network_comparison
1	no value	Measured	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]	Subtracted	High confidence	41482.5	33356.5	8126
	CPD		carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976]		Low confidence	40899	32028.5	8870.5
		Ranked		Divided		16	32	2
		Squared		Subtracted		395912	242799	153113
	HLX	Ranked	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]		High confidence	215	322	107
	LAMP1	Measured	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	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
	RINT1	Measured	rad50-interacting protein 1. [refseq;acc:nm_021930]	Divided	High confidence	450.5	2394.5	5.31521
		Squared				48.0356	1357.07	28.2513
		Rooted				21.225	48.9336	2.30547
				Subtracted				27.7086
	UBAC1	Ranked	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	Divided		10	24	2.4
		Squared		Subtracted		468498	322755	145743
2	no value	Ranked	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		15	28	1.86667
		Squared		Subtracted		407289	263351	143938
	BEST1		bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090]		Low confidence	333556	475119	141563
	CDK4	Measured	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	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
	HBS1L	Ranked	hbs1-like. [refseq;acc:nm_006620]		High confidence	215	322	107
	LAMP1		lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	Divided	Low confidence	223	330	1.47982
	MRPS17	Measured	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	Subtracted		21185	28492	7307
	PSCD1		cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]		High confidence	41482.5	33356.5	8126
	RHOBTB2		rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	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	BEST4	Squared	vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274]		Low confidence	333506	475045	141539
	CDK4	Ranked	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	Divided		223	330	1.47982
	CDK6	Measured	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]			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
	HLX	Measured	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	Divided	High confidence	2597.5	698.5	3.71868
		Squared				1596.92	115.48	13.8285
		Rooted				50.9657	26.4292	1.92839
				Subtracted				24.5365
	PSCD1	Ranked	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	Divided		15	28	1.86667
		Squared		Subtracted		407289	263351	143938
	PSCD2	Measured	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]			41482.5	33356.5	8126
	RINT1	Ranked	rad50-interacting protein 1. [refseq;acc:nm_021930]			337	232	105
	SLC25A43	Measured	mitochondrial solute carrier protein. [refseq;acc:nm_145305]		Low confidence	21185	28492	7307
4	no value	Squared	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]			332411	473408	140997
	BEST1	Measured	bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090]			36474.3	43509.4	7035.1

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.