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

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Showing element 1 to 50 of 38536 in total

Network Comparison Type  : Divided

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

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.