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

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Showing element 451 to 500 of 29840 in total

Interaction Map  : High confidence

description	Rank	Value Type	Filtered	Network Comparison Type	green	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	Ranked	1	Divided	0.00001	0.00001	1
				Subtracted	0	0	0
		Squared		Divided	0.00001	0.00001	1
				Subtracted	0	0	0
		Rooted		Divided	0.00001	0.00001	1
				Subtracted	0	0	0
3-hydroxyanthranilate 3,4-dioxygenase (ec 1.13.11.6) (3-hao) (3-hydroxyanthranilic acid dioxygenase) (3-hydroxyanthranilate oxygenase). [swissprot;acc:p46952]	1664				69.3348	67.2158	2.119
	1764			Divided			1.03153
	1826	Measured		Subtracted	7295.24	6916.14	379.1
	2105			Divided			1.05481
	2189	Ranked			208.162	209.54	1.00662
	2201			Subtracted			1.378
	2541	Squared			36579.1	35558.6	1020.5
	2642			Divided			1.0287
3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362]	262		0	Subtracted	18218.3	18353.1	134.8
	321	Measured			2853.65	2925.57	71.92
	327	Ranked		Divided	10466.5	9897.29	1.05751
	347	Rooted		Subtracted	31.1453	32.3671	1.2218
	348	Ranked			10466.5	9897.29	569.21
	376	Rooted		Divided	31.1453	32.3671	1.03923
	438	Measured			2853.65	2925.57	1.0252
	477	Squared			18218.3	18353.1	1.0074
	544		1	Subtracted	32866.2	27898	4968.2
	646			Divided			1.17808
	1543	Measured		Subtracted	7317.48	6885.11	432.37
	1852	Ranked		Divided	198.154	196.008	1.01095
	1898	Measured			7317.48	6885.11	1.0628
	1914	Ranked		Subtracted	198.154	196.008	2.146
	2369	Rooted			71.371	70.3295	1.0415
	2412			Divided			1.01481
3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [swissprot;acc:p09110]	239	Squared	0	Subtracted	6794.39	6970.13	175.74
	264	Measured			1721.76	1837.26	115.5
	339	Rooted			26.8141	28.0711	1.257
	346	Measured		Divided	1721.76	1837.26	1.06708
	357	Rooted			26.8141	28.0711	1.04688
	455	Squared			6794.39	6970.13	1.02587
	473	Ranked		Subtracted	10243.1	10156.4	86.7
	478			Divided			1.00854
	840	Squared	1	Subtracted	31125.2	27235.1	3890.1
	1116			Divided			1.14283
	2061	Measured		Subtracted	7263.87	6946.82	317.05
	2300	Ranked		Divided	192.541	191.563	1.00511
	2305	Measured			7263.87	6946.82	1.04564
	2331	Ranked		Subtracted	192.541	191.563	0.978
	2473	Rooted			72.2607	71.4427	0.818
	2490			Divided			1.01145
3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325]	515	Squared			23960.7	19987.6	1.19878
	563	Measured			6222.04	5480.24	1.13536
	615			Subtracted			741.8
	767	Rooted		Divided	67.7402	63.5181	1.06647

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.