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

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

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.