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

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Showing element 501 to 550 of 38536 in total

Network Comparison Type  : Divided

description	Rank	Filtered	green	Value Type	Interaction Map	network_comparison	red
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]	3180	1	0.00001	Rooted	High confidence	1	0.00001
	3728		8094.29	Measured	Low confidence	1.02451	7900.62
	3855		73.5484	Rooted		1.02832	71.5231
	4091		200.093	Ranked		1.01094	202.282
3-hydroxyanthranilate 3,4-dioxygenase (ec 1.13.11.6) (3-hao) (3-hydroxyanthranilic acid dioxygenase) (3-hydroxyanthranilate oxygenase). [swissprot;acc:p46952]	111		74962.3	Squared		1.15248	65044.3
	143		11639.5	Measured		1.08815	10696.6
	399		88.7007	Rooted		1.04795	84.6421
	1250		176.667	Ranked		1.02263	180.665
	1764		69.3348	Rooted	High confidence	1.03153	67.2158
	2105		7295.24	Measured		1.05481	6916.14
	2189		208.162	Ranked		1.00662	209.54
	2642		36579.1	Squared		1.0287	35558.6
3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362]	327	0	10466.5	Ranked		1.05751	9897.29
	376		31.1453	Rooted		1.03923	32.3671
	438		2853.65	Measured		1.0252	2925.57
	442		25.4539	Rooted	Low confidence	1.06963	27.2263
	477		18218.3	Squared	High confidence	1.0074	18353.1
	501		11352.1	Ranked	Low confidence	1.0588	10721.7
	581		1932.95	Measured		1.04278	2015.65
	646	1	32866.2	Squared	High confidence	1.17808	27898
	703	0	10485.1		Low confidence	1.03494	10851.4
	879	1	198.284	Ranked		1.02557	203.354
	1052		74.3827	Rooted		1.03876	71.6074
	1660		8232.52	Measured		1.0334	7966.46
	1852		198.154	Ranked	High confidence	1.01095	196.008
	1898		7317.48	Measured		1.0628	6885.11
	2412		71.371	Rooted		1.01481	70.3295
	3343		43619.2	Squared	Low confidence	1.03355	45082.7
3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [swissprot;acc:p09110]	346	0	1721.76	Measured	High confidence	1.06708	1837.26
	357		26.8141	Rooted		1.04688	28.0711
	455		6794.39	Squared		1.02587	6970.13
	459		1500.63	Measured	Low confidence	1.07746	1616.87
	461		24.5318	Rooted		1.0647	26.1189
	478		10243.1	Ranked	High confidence	1.00854	10156.4
	614		10984.2		Low confidence	1.03221	10641.4
	655		5250.39	Squared		1.05066	5516.4
	1116	1	31125.2		High confidence	1.14283	27235.1
	2300		192.541	Ranked		1.00511	191.563
	2305		7263.87	Measured		1.04564	6946.82
	2490		72.2607	Rooted		1.01145	71.4427
	2649		192.486	Ranked	Low confidence	1.01776	195.904
	3780		8366.35	Measured		1.02419	8168.73
	3866		75.8932	Rooted		1.02825	73.8081
	3876		43332.8	Squared		1.02955	44613.5
3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325]	515		23960.7		High confidence	1.19878	19987.6
	563		6222.04	Measured		1.13536	5480.24
	767		67.7402	Rooted		1.06647	63.5181
	1025		199.266	Ranked		1.03195	205.632
	2218		8689.87	Measured	Low confidence	1.03137	8425.53
	2252		192.92	Ranked		1.01888	196.562

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.