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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 14920 in total

Network Comparison Type  : Divided
Interaction Map  : High confidence

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

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.