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

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Showing element 1 to 50 of 66312 in total

Filtered  : 1

Rank	Hugo	description	Network Comparison Type	Value Type	Interaction Map	red	network_comparison	green
1	no value	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	Measured	High confidence	41482.5	8126	33356.5
	CPD	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976]	Divided	Ranked	Low confidence	16	2	32
			Subtracted	Measured		40899	8870.5	32028.5
				Squared		395912	153113	242799
	HLX	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]		Ranked	High confidence	215	107	322
	LAMP1	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	Divided	Measured	Low confidence	2399.5	4.4149	543.5
				Squared		1362.75	19.4914	69.9153
				Rooted		48.9847	2.10117	23.3131
			Subtracted	Ranked		223	107	330
				Rooted		48.9847	25.6716	23.3131
	RINT1	rad50-interacting protein 1. [refseq;acc:nm_021930]	Divided	Measured	High confidence	450.5	5.31521	2394.5
				Squared		48.0356	28.2513	1357.07
				Rooted		21.225	2.30547	48.9336
			Subtracted				27.7086
	UBAC1	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	Divided	Ranked		10	2.4	24
			Subtracted	Squared		468498	145743	322755
2	no value	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	Ranked		15	1.86667	28
			Subtracted	Squared		407289	143938	263351
	BEST1	bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090]			Low confidence	333556	141563	475119
	CDK4	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	Divided	Measured		2399.5	4.4149	543.5
				Squared		1362.75	19.4914	69.9153
				Rooted		48.9847	2.10117	23.3131
			Subtracted	Ranked		223	107	330
				Rooted		48.9847	25.6716	23.3131
	HBS1L	hbs1-like. [refseq;acc:nm_006620]		Ranked	High confidence	215	107	322
	LAMP1	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	Divided		Low confidence	223	1.47982	330
	MRPS17	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	Subtracted	Measured		21185	7307	28492
	PSCD1	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]			High confidence	41482.5	8126	33356.5
	RHOBTB2	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	Divided			450.5	5.31521	2394.5
				Squared		48.0356	28.2513	1357.07
				Rooted		21.225	2.30547	48.9336
			Subtracted				27.7086
3	BEST4	vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274]		Squared	Low confidence	333506	141539	475045
	CDK4	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	Divided	Ranked		223	1.47982	330
	CDK6	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]		Measured		2399.5	4.4149	543.5
				Squared		1362.75	19.4914	69.9153
				Rooted		48.9847	2.10117	23.3131
			Subtracted	Ranked		223	107	330
				Rooted		48.9847	25.6716	23.3131
	HLX	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	Divided	Measured	High confidence	2597.5	3.71868	698.5
				Squared		1596.92	13.8285	115.48
				Rooted		50.9657	1.92839	26.4292
			Subtracted				24.5365
	PSCD1	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	Divided	Ranked		15	1.86667	28
			Subtracted	Squared		407289	143938	263351
	PSCD2	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]		Measured		41482.5	8126	33356.5
	RINT1	rad50-interacting protein 1. [refseq;acc:nm_021930]		Ranked		337	105	232
	SLC25A43	mitochondrial solute carrier protein. [refseq;acc:nm_145305]		Measured	Low confidence	21185	7307	28492
4	no value	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]		Squared		332411	140997	473408
	BEST1	bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090]		Measured		36474.3	7035.1	43509.4

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.