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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 14920 in total

Network Comparison Type  : Divided
Interaction Map  : High confidence

Rank	description	Value Type	Filtered	green	red	network_comparison
1	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	Ranked	0	15915	4294	3.70633
	cab2. [refseq;acc:nm_033419]	Squared		7.16592	0.00001	716592
	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Measured		0.00001	364	36400000
		Rooted			19.0788	1907880
	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	Ranked	1	24	10	2.4
	rad50-interacting protein 1. [refseq;acc:nm_021930]	Measured		2394.5	450.5	5.31521
		Squared		1357.07	48.0356	28.2513
		Rooted		48.9336	21.225	2.30547
2	cab2. [refseq;acc:nm_033419]	Measured	0	174	0.00001	17400000
	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	15	1.86667
	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]		0	14977	5865	2.55362
	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	Squared		0.00001	5.61325	561325
		Rooted			12.4097	1240970
	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	Measured	1	2394.5	450.5	5.31521
		Squared		1357.07	48.0356	28.2513
		Rooted		48.9336	21.225	2.30547
3	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	Ranked		28	15	1.86667
	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	Measured		698.5	2597.5	3.71868
		Squared		115.48	1596.92	13.8285
		Rooted		26.4292	50.9657	1.92839
	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	Ranked	0	11083.9	4475.84	2.47638
	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	Measured		109	0.00001	10900000
	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	Squared		0.00001	5.61325	561325
		Rooted			12.4097	1240970
4	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	Ranked	1	28	15	1.86667
	hbs1-like. [refseq;acc:nm_006620]	Measured		698.5	2597.5	3.71868
		Squared		115.48	1596.92	13.8285
		Rooted		26.4292	50.9657	1.92839
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Measured	0	89	0.00001	8900000
	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Ranked		21883	8906	2.45711
	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	Squared		2.81207	0.00001	281207
		Rooted		10.4403		1044030
5	cytohesin 4. [swissprot;acc:q9uia0]	Ranked	1	28	15	1.86667
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Squared	0	1.87479	0.00001	187479
		Rooted		9.43398		943398
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Measured		89		8900000
	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]		1	339.5	1153.5	3.39764
		Squared		27.2805	314.926	11.544
		Rooted		18.4255	33.9632	1.84327
	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]	Ranked	0	11965.7	5510.5	2.17144
6	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]		1	28	15	1.86667
	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Measured	0	89	0.00001	8900000
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Squared		1.87479		187479
		Rooted		9.43398		943398
	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	Measured	1	339.5	1153.5	3.39764
		Squared		27.2805	314.926	11.544
		Rooted		18.4255	33.9632	1.84327
	ubiquitin protein ligase. [refseq;acc:nm_130466]	Ranked	0	15339.2	7523	2.03897
7	cab2. [refseq;acc:nm_033419]			10950	21866	1.99689
	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]		1	322	215	1.49767

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.