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

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Showing element 451 to 500 of 38536 in total

Network Comparison Type  : Divided

description	Filtered	Rank	Value Type	green	Interaction Map	network_comparison	red
3 beta-hydroxy-delta 5-c27-steroid oxidoreductase. [refseq;acc:nm_025193]	1	2627	Rooted	75.4487	Low confidence	1.03326	73.0199
		3147	Measured	0.00001	High confidence	1	0.00001
			Ranked
			Squared
			Rooted
		3493	Measured	8292.57	Low confidence	1.02604	8082.12
3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8]	0	299	Ranked	11512.3	High confidence	1.07178	12338.7
		438	Rooted	44.9836		1.025	43.8864
		453	Ranked	11512.3	Low confidence	1.07178	12338.7
		492	Measured	5046.33	High confidence	1.00159	5038.33
		493	Squared	17901.1		1	17901.1
		662	Rooted	44.9836	Low confidence	1.025	43.8864
		822	Measured	5046.33		1.00159	5038.33
		836	Squared	17901.1		1	17901.1
	1	1073		42724.1		1.04712	44737.4
		1663	Ranked	193.866		1.02066	197.872
		2622	Rooted	75.4487		1.03326	73.0199
		2756	Measured	0.00001	High confidence	1	0.00001
			Ranked
			Squared
			Rooted
		3487	Measured	8292.57	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	Squared	42724.1		1.04712	44737.4
		1665	Ranked	193.866		1.02066	197.872
		2624	Rooted	75.4487		1.03326	73.0199
		2802	Measured	0.00001	High confidence	1	0.00001
			Ranked
			Squared
			Rooted
		3489	Measured	8292.57	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	Ranked	221.607		1.0555	209.954
		2650	Squared	36053.6		1.03756	37407.8
		4603	Rooted	65.5857		1.02069	66.9425
		4994	Measured	6911.72		1.0016	6922.79
3'-5' rna exonuclease; polynucleotide phosphorylase-like. [refseq;acc:nm_033109]		1373	Ranked	201.696		1.02198	206.13
		1388	Rooted	72.4192		1.03696	69.8381
		2310	Measured	7838.4		1.03105	7602.32
		2740	Squared	41084.3		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	Measured	7263.68		1.04565	6946.6
		2303	Ranked	192.542		1.00509	191.567
		2488	Rooted	72.2598		1.01146	71.4412
		3121	Squared	43211.7	Low confidence	1.03483	44716.9
		3261	Ranked	196.642		1.01577	199.744
		3321	Measured	8238.4		1.02679	8023.42
		3423	Rooted	74.7129		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	Squared	43022.5		1.04104	44788.1
		3180	Measured	0.00001	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.