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

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Showing element 501 to 550 of 38536 in total

Network Comparison Type  : Divided

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

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.