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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 14920 in total

Interaction Map  : High confidence
Network Comparison Type  : Divided

Rank	Filtered	Value Type	description	red	green	network_comparison
1	0	Measured	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	364	0.00001	36400000
		Ranked	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	4294	15915	3.70633
		Squared	cab2. [refseq;acc:nm_033419]	0.00001	7.16592	716592
		Rooted	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	19.0788	0.00001	1907880
	1	Measured	rad50-interacting protein 1. [refseq;acc:nm_021930]	450.5	2394.5	5.31521
		Ranked	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	10	24	2.4
		Squared	rad50-interacting protein 1. [refseq;acc:nm_021930]	48.0356	1357.07	28.2513
		Rooted		21.225	48.9336	2.30547
2	0	Measured	cab2. [refseq;acc:nm_033419]	0.00001	174	17400000
		Ranked	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	5865	14977	2.55362
		Squared	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	5.61325	0.00001	561325
		Rooted		12.4097		1240970
	1	Measured	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	450.5	2394.5	5.31521
		Ranked	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]	15	28	1.86667
		Squared	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	48.0356	1357.07	28.2513
		Rooted		21.225	48.9336	2.30547
3	0	Measured	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	0.00001	109	10900000
		Ranked	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	4475.84	11083.9	2.47638
		Squared	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	5.61325	0.00001	561325
		Rooted		12.4097		1240970
	1	Measured	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	2597.5	698.5	3.71868
		Ranked	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	15	28	1.86667
		Squared	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	1596.92	115.48	13.8285
		Rooted		50.9657	26.4292	1.92839
4	0	Measured	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	0.00001	89	8900000
		Ranked	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	8906	21883	2.45711
		Squared	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	0.00001	2.81207	281207
		Rooted			10.4403	1044030
	1	Measured	hbs1-like. [refseq;acc:nm_006620]	2597.5	698.5	3.71868
		Ranked	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	15	28	1.86667
		Squared	hbs1-like. [refseq;acc:nm_006620]	1596.92	115.48	13.8285
		Rooted		50.9657	26.4292	1.92839
5	0	Measured	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	0.00001	89	8900000
		Ranked	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]	5510.5	11965.7	2.17144
		Squared	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	0.00001	1.87479	187479
		Rooted			9.43398	943398
	1	Measured	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	1153.5	339.5	3.39764
		Ranked	cytohesin 4. [swissprot;acc:q9uia0]	15	28	1.86667
		Squared	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	314.926	27.2805	11.544
		Rooted		33.9632	18.4255	1.84327
6	0	Measured	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	0.00001	89	8900000
		Ranked	ubiquitin protein ligase. [refseq;acc:nm_130466]	7523	15339.2	2.03897
		Squared	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	0.00001	1.87479	187479
		Rooted			9.43398	943398
	1	Measured	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	1153.5	339.5	3.39764
		Ranked	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	15	28	1.86667
		Squared	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	314.926	27.2805	11.544
		Rooted		33.9632	18.4255	1.84327
7	0	Measured	sedlin. [swissprot;acc:o14582]	0.00001	43	4300000
		Ranked	cab2. [refseq;acc:nm_033419]	21866	10950	1.99689

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.