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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 14920 in total

Network Comparison Type  : Divided
Interaction Map  : High confidence

Rank	Filtered	description	green	Value Type	red	network_comparison
1	0	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	15915	Ranked	4294	3.70633
		cab2. [refseq;acc:nm_033419]	7.16592	Squared	0.00001	716592
		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0.00001	Measured	364	36400000
				Rooted	19.0788	1907880
	1	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	24	Ranked	10	2.4
		rad50-interacting protein 1. [refseq;acc:nm_021930]	48.9336	Rooted	21.225	2.30547
			1357.07	Squared	48.0356	28.2513
			2394.5	Measured	450.5	5.31521
2	0	cab2. [refseq;acc:nm_033419]	174		0.00001	17400000
		mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	14977	Ranked	5865	2.55362
		nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	0.00001	Squared	5.61325	561325
				Rooted	12.4097	1240970
	1	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	Ranked	15	1.86667
		rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	48.9336	Rooted	21.225	2.30547
			1357.07	Squared	48.0356	28.2513
			2394.5	Measured	450.5	5.31521
3	0	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	11083.9	Ranked	4475.84	2.47638
		pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	109	Measured	0.00001	10900000
		transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	0.00001	Squared	5.61325	561325
				Rooted	12.4097	1240970
	1	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	28	Ranked	15	1.86667
		homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	26.4292	Rooted	50.9657	1.92839
			115.48	Squared	1596.92	13.8285
			698.5	Measured	2597.5	3.71868
4	0	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	89		0.00001	8900000
		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	21883	Ranked	8906	2.45711
		pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	2.81207	Squared	0.00001	281207
			10.4403	Rooted		1044030
	1	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	28	Ranked	15	1.86667
		hbs1-like. [refseq;acc:nm_006620]	26.4292	Rooted	50.9657	1.92839
			115.48	Squared	1596.92	13.8285
			698.5	Measured	2597.5	3.71868
5	0	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	1.87479	Squared	0.00001	187479
			9.43398	Rooted		943398
		homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	89	Measured		8900000
		ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]	11965.7	Ranked	5510.5	2.17144
	1	cytohesin 4. [swissprot;acc:q9uia0]	28		15	1.86667
		junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	18.4255	Rooted	33.9632	1.84327
			27.2805	Squared	314.926	11.544
			339.5	Measured	1153.5	3.39764
6	0	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	89		0.00001	8900000
		homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	1.87479	Squared		187479
			9.43398	Rooted		943398
		ubiquitin protein ligase. [refseq;acc:nm_130466]	15339.2	Ranked	7523	2.03897
	1	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	28		15	1.86667
		junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	18.4255	Rooted	33.9632	1.84327
			27.2805	Squared	314.926	11.544
			339.5	Measured	1153.5	3.39764
7	0	cab2. [refseq;acc:nm_033419]	10950	Ranked	21866	1.99689
		homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	1.87479	Squared	0.00001	187479

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.