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

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Showing element 1 to 50 of 38536 in total

Network Comparison Type  : Divided

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