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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 38536 in total

Network Comparison Type  : Divided

Rank	Interaction Map	description	Value Type	Filtered	green	network_comparison	red
1	High confidence	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	Ranked	0	15915	3.70633	4294
		cab2. [refseq;acc:nm_033419]	Squared		7.16592	716592	0.00001
		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Measured		0.00001	36400000	364
			Rooted			1907880	19.0788
		putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	Ranked	1	24	2.4	10
		rad50-interacting protein 1. [refseq;acc:nm_021930]	Measured		2394.5	5.31521	450.5
			Squared		1357.07	28.2513	48.0356
			Rooted		48.9336	2.30547	21.225
	Low confidence	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976]	Ranked		32	2	16
		homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Squared	0	1.87479	187479	0.00001
		lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	Measured	1	543.5	4.4149	2399.5
			Squared		69.9153	19.4914	1362.75
			Rooted		23.3131	2.10117	48.9847
		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Measured	0	0.00001	36400000	364
			Rooted			1907880	19.0788
		mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	Ranked		14977	2.55362	5865
2	High confidence	cab2. [refseq;acc:nm_033419]	Measured		174	17400000	0.00001
		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]	Ranked	1	28	1.86667	15
		mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]		0	14977	2.55362	5865
		nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	Squared		0.00001	561325	5.61325
			Rooted			1240970	12.4097
		rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	Measured	1	2394.5	5.31521	450.5
			Squared		1357.07	28.2513	48.0356
			Rooted		48.9336	2.30547	21.225
	Low confidence	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	Measured		543.5	4.4149	2399.5
			Squared		69.9153	19.4914	1362.75
			Rooted		23.3131	2.10117	48.9847
		homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Measured	0	89	8900000	0.00001
			Rooted		9.43398	943398
		homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Squared		1.87479	187479
		lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	Ranked	1	330	1.47982	223
		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]		0	21883	2.45711	8906
3	High confidence	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]		1	28	1.86667	15
		homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	Measured		698.5	3.71868	2597.5
			Squared		115.48	13.8285	1596.92
			Rooted		26.4292	1.92839	50.9657
		nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	Ranked	0	11083.9	2.47638	4475.84
		pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	Measured		109	10900000	0.00001
		transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	Squared		0.00001	561325	5.61325
			Rooted			1240970	12.4097
	Low confidence	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	Ranked	1	330	1.47982	223
		cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]	Measured		543.5	4.4149	2399.5
			Squared		69.9153	19.4914	1362.75
			Rooted		23.3131	2.10117	48.9847
		homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Squared	0	1.87479	187479	0.00001
		homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Measured		89	8900000
			Rooted		9.43398	943398
		neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]	Ranked		20617	2.14604	9607
4	High confidence	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]		1	28	1.86667	15
		hbs1-like. [refseq;acc:nm_006620]	Measured		698.5	3.71868	2597.5

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.