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

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Showing element 1 to 50 of 38536 in total

Network Comparison Type  : Divided

Rank	green	Filtered	Value Type	Interaction Map	description	network_comparison	red
1	0.00001	0	Measured	High confidence	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	36400000	364
				Low confidence
			Rooted	High confidence		1907880	19.0788
				Low confidence
	1.87479		Squared		homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	187479	0.00001
	7.16592			High confidence	cab2. [refseq;acc:nm_033419]	716592
	23.3131	1	Rooted	Low confidence	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	2.10117	48.9847
	24		Ranked	High confidence	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	2.4	10
	32			Low confidence	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976]	2	16
	48.9336		Rooted	High confidence	rad50-interacting protein 1. [refseq;acc:nm_021930]	2.30547	21.225
	69.9153		Squared	Low confidence	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	19.4914	1362.75
	543.5		Measured			4.4149	2399.5
	1357.07		Squared	High confidence	rad50-interacting protein 1. [refseq;acc:nm_021930]	28.2513	48.0356
	2394.5		Measured			5.31521	450.5
	14977	0	Ranked	Low confidence	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	2.55362	5865
	15915			High confidence	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	3.70633	4294
2	0.00001		Squared		nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	561325	5.61325
			Rooted			1240970	12.4097
	1.87479		Squared	Low confidence	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	187479	0.00001
	9.43398		Rooted		homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	943398
	23.3131	1			cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	2.10117	48.9847
	28		Ranked	High confidence	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]	1.86667	15
	48.9336		Rooted		rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	2.30547	21.225
	69.9153		Squared	Low confidence	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	19.4914	1362.75
	89	0	Measured		homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	8900000	0.00001
	174			High confidence	cab2. [refseq;acc:nm_033419]	17400000
	330	1	Ranked	Low confidence	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	1.47982	223
	543.5		Measured		cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	4.4149	2399.5
	1357.07		Squared	High confidence	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	28.2513	48.0356
	2394.5		Measured			5.31521	450.5
	14977	0	Ranked		mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	2.55362	5865
	21883			Low confidence	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	2.45711	8906
3	0.00001		Squared	High confidence	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	561325	5.61325
			Rooted			1240970	12.4097
	1.87479		Squared	Low confidence	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	187479	0.00001
	9.43398		Rooted		homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	943398
	23.3131	1			cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]	2.10117	48.9847
	26.4292			High confidence	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	1.92839	50.9657
	28		Ranked		cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	1.86667	15
	69.9153		Squared	Low confidence	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]	19.4914	1362.75
	89	0	Measured		homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	8900000	0.00001
	109			High confidence	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	10900000
	115.48	1	Squared		homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	13.8285	1596.92
	330		Ranked	Low confidence	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	1.47982	223
	543.5		Measured		cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]	4.4149	2399.5
	698.5			High confidence	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	3.71868	2597.5
	11083.9	0	Ranked		nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	2.47638	4475.84
	20617			Low confidence	neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]	2.14604	9607
4	0.823905		Squared		guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [swissprot;acc:q9byb4]	82390.5	0.00001
	2.81207			High confidence	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	281207

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.