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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.

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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 77072 in total

Rank	description	Value Type	Network Comparison Type	Interaction Map	Filtered	green	red	network_comparison
1	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	Ranked	Divided	High confidence	0	15915	4294	3.70633
	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	Measured	Subtracted			6410	85	6325
				Low confidence
		Rooted		High confidence		60.0707	9.20014	50.8706
				Low confidence
	cab2. [refseq;acc:nm_033419]	Squared	Divided	High confidence		7.16592	0.00001	716592
	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976]	Measured	Subtracted	Low confidence	1	32028.5	40899	8870.5
		Ranked	Divided			32	16	2
		Squared	Subtracted			242799	395912	153113
	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	Ranked		High confidence		322	215	107
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Squared	Divided	Low confidence	0	1.87479	0.00001	187479
	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	Measured			1	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
	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		33356.5	41482.5	8126
	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]		Divided		0	0.00001	364	36400000
				Low confidence
		Ranked	Subtracted	High confidence		21883	8906	12977
				Low confidence
		Rooted	Divided	High confidence		0.00001	19.0788	1907880
				Low confidence
	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	Ranked				14977	5865	2.55362
	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Squared	Subtracted	High confidence		160184	232467	72283
				Low confidence
	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	Ranked	Divided	High confidence	1	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		Low confidence		28492	21185	7307
	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	Ranked		High confidence	0	15915	4294	11621
	bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090]	Squared		Low confidence	1	475119	333556	141563
	cab2. [refseq;acc:nm_033419]	Measured	Divided	High confidence	0	174	0.00001	17400000
	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]			Low confidence	1	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		High confidence		33356.5	41482.5	8126
	hbs1-like. [refseq;acc:nm_006620]	Ranked				322	215	107
	histone h4. [swissprot;acc:p02304]	Squared			0	345123	273623	71500
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Measured	Divided	Low confidence		89	0.00001	8900000
		Rooted				9.43398		943398
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Squared				1.87479		187479
	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	Measured	Subtracted	High confidence		6410	85	6325
		Rooted				60.0707	9.20014	50.8706
	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	Ranked	Divided	Low confidence	1	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.