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

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Showing element 451 to 500 of 38536 in total

Network Comparison Type  : Divided

description	Filtered	Rank	green	Value Type	Interaction Map	network_comparison	red
3 beta-hydroxy-delta 5-c27-steroid oxidoreductase. [refseq;acc:nm_025193]	1	2627	75.4487	Rooted	Low confidence	1.03326	73.0199
		3147	0.00001	Measured	High confidence	1	0.00001
				Ranked
				Squared
				Rooted
		3493	8292.57	Measured	Low confidence	1.02604	8082.12
3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8]	0	299	11512.3	Ranked	High confidence	1.07178	12338.7
		438	44.9836	Rooted		1.025	43.8864
		453	11512.3	Ranked	Low confidence	1.07178	12338.7
		492	5046.33	Measured	High confidence	1.00159	5038.33
		493	17901.1	Squared		1	17901.1
		662	44.9836	Rooted	Low confidence	1.025	43.8864
		822	5046.33	Measured		1.00159	5038.33
		836	17901.1	Squared		1	17901.1
	1	1073	42724.1			1.04712	44737.4
		1663	193.866	Ranked		1.02066	197.872
		2622	75.4487	Rooted		1.03326	73.0199
		2756	0.00001	Measured	High confidence	1	0.00001
				Ranked
				Squared
				Rooted
		3487	8292.57	Measured	Low confidence	1.02604	8082.12
3 beta-hydroxysteroid dehydrogenase/delta 5-->4-isomerase type i (3beta-hsd i) (trophoblast antigen fdo161g) [includes: 3-beta-hydroxy- delta(5)-steroid dehydrogenase (ec 1.1.1.145) (3-beta-hydroxy-5-ene steroid dehydrogenase) (progesterone reductase); steroid delta- isomerase (ec 5.3.3.1) (delta-5-3-ketosteroid isomerase)]. [swissprot;acc:p14060]		1075	42724.1	Squared		1.04712	44737.4
		1665	193.866	Ranked		1.02066	197.872
		2624	75.4487	Rooted		1.03326	73.0199
		2802	0.00001	Measured	High confidence	1	0.00001
				Ranked
				Squared
				Rooted
		3489	8292.57	Measured	Low confidence	1.02604	8082.12
3'(2'), 5'-bisphosphate nucleotidase 1; bisphosphate 3'-nucleotidase; bpntase; pap-inositol-1,4-phosphatase. [refseq;acc:nm_006085]		178	221.607	Ranked		1.0555	209.954
		2650	36053.6	Squared		1.03756	37407.8
		4603	65.5857	Rooted		1.02069	66.9425
		4994	6911.72	Measured		1.0016	6922.79
3'-5' rna exonuclease; polynucleotide phosphorylase-like. [refseq;acc:nm_033109]		1373	201.696	Ranked		1.02198	206.13
		1388	72.4192	Rooted		1.03696	69.8381
		2310	7838.4	Measured		1.03105	7602.32
		2740	41084.3	Squared		1.03707	42607.1
3-hydroxy-3-methylglutaryl-coenzyme a reductase (ec 1.1.1.34) (hmg-coa reductase). [swissprot;acc:p04035]		1118	31123.3		High confidence	1.1428	27234.2
		2302	7263.68	Measured		1.04565	6946.6
		2303	192.542	Ranked		1.00509	191.567
		2488	72.2598	Rooted		1.01146	71.4412
		3121	43211.7	Squared	Low confidence	1.03483	44716.9
		3261	196.642	Ranked		1.01577	199.744
		3321	8238.4	Measured		1.02679	8023.42
		3423	74.7129	Rooted		1.03051	72.5008
3-hydroxyacyl-coa dehydrogenase type ii (ec 1.1.1.35) (type ii hadh) (endoplasmic reticulum-associated amyloid beta-peptide binding protein) (short-chain type dehydrogenase/reductase xh98g2). [swissprot;acc:q99714]		1886	43022.5	Squared		1.04104	44788.1
		3180	0.00001	Measured	High confidence	1	0.00001
				Ranked
				Squared

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.