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

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Showing element 401 to 450 of 77072 in total

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description	Value Type	Rank	Network Comparison Type	network_comparison	Interaction Map	green	red
60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025]	Squared	134	Subtracted	901.95	High confidence	4339.96	3438.01
		253		762.43	Low confidence	5282.62	4520.19
		259	Divided	1.26235	High confidence	4339.96	3438.01
		307		1.16867	Low confidence	5282.62	4520.19
	Rooted	334	Subtracted	1.3001	High confidence	28.9062	27.6061
		355	Divided	1.04709
		696	Subtracted	0.5228	Low confidence	26.2823	25.7595
		698	Divided	1.0203
60s ribosomal protein l12 like protein. [sptrembl;acc:o60886]	Measured	215	Subtracted	147.29	High confidence	1805.52	1658.23
		330	Divided	1.08882
		340	Subtracted	144.34	Low confidence	1804.55	1660.21
		426	Divided	1.08694
	Ranked	396		1.03436	High confidence	9856.12	10194.8
		408	Subtracted	338.68
		724	Divided	1.01502	Low confidence	10529.4	10373.6
		731	Subtracted	155.8
	Squared	128		953.08	High confidence	4640.77	3687.69
		194		1122.16	Low confidence	5457.07	4334.91
		235	Divided	1.25887
		265		1.25845	High confidence	4640.77	3687.69
	Rooted	343	Subtracted	1.2362		28.7604	27.5242
		362	Divided	1.04491
		740	Subtracted	0.3688	Low confidence	27.2559	26.8871
		744	Divided	1.01372
60s ribosomal protein l12. [swissprot;acc:p30050]	Measured	217	Subtracted	147.27	High confidence	1805.05	1657.78
		328	Divided	1.08884
		346	Subtracted	143.9	Low confidence	1803.39	1659.49
		428	Divided	1.08671
	Ranked	394		1.0344	High confidence	9857.79	10196.9
		406	Subtracted	339.11
		723	Divided	1.01502	Low confidence	10530.4	10374.6
		730	Subtracted	155.8
	Squared	130		952.81	High confidence	4639.46	3686.65
		196		1120.74	Low confidence	5452.56	4331.82
		237	Divided	1.25872
		264		1.25845	High confidence	4639.46	3686.65
	Rooted	341	Subtracted	1.2364		28.7547	27.5183
		360	Divided	1.04493
		742	Subtracted	0.3653	Low confidence	27.2466	26.8813
		748	Divided	1.01359
60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914]	Measured	392		1.04238	High confidence	219.891	229.211
		452	Subtracted	9.32
		647		37.25	Low confidence	3735.24	3772.49
		773	Divided	1.00997
	Ranked	239	Subtracted	1075.8		10927.4	12003.2
		345	Divided	1.09845
		423	Subtracted	312.8	High confidence	12631.5	12318.7
		429	Divided	1.02539
	Squared	72	Subtracted	3610.7	Low confidence	42399.1	46009.8
		331	Divided	1.14497	High confidence	22.8932	26.2121

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.