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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description	Value Type	Rank	Network Comparison Type	network_comparison	Interaction Map	green	red
alpha 2 globin. [refseq;acc:nm_000517]	Measured	602	Divided	1.03569	Low confidence	1066.67	1104.74
		643	Subtracted	38.07
	Ranked	19		4500.9		15987.1	11486.2
		30	Divided	1.39185
	Squared	281	Subtracted	631.92		7479.85	6847.93
		545	Divided	1.09228
	Rooted	53	Subtracted	5.4015		12.9538	18.3553
		67	Divided	1.41698
alpha crystallin a chain. [swissprot;acc:p02489]	Measured	86		1.61366	High confidence	89.2447	55.3059
		390	Subtracted	33.9388
		559		57.45	Low confidence	1749.08	1806.53
		619	Divided	1.03285
	Ranked	86	Subtracted	2400.2	High confidence	13972.2	16372.4
		139	Divided	1.17178
		656		1.02341	Low confidence	11069.9	11329
		661	Subtracted	259.1
	Squared	121	Divided	1.89488	High confidence	2.40686	1.27019
		371	Subtracted	360.79	Low confidence	7807.66	7446.87
		444		1.13667	High confidence	2.40686	1.27019
		664	Divided	1.04845	Low confidence	7807.66	7446.87
	Rooted	68		1.38766	High confidence	8.63381	6.22183
		239	Subtracted	2.41198
		565	Divided	1.04168	Low confidence	24.6113	25.637
		575	Subtracted	1.0257
alpha-1-acid glycoprotein 2 precursor (agp 2) (orosomucoid 2) (omd 2). [swissprot;acc:p19652]	Measured	435		16.74	High confidence	2335.98	2319.24
		475	Divided	1.00722
		496	Subtracted	75.49	Low confidence	1742.4	1817.89
		577	Divided	1.04333
	Ranked	215	Subtracted	1190		11679.4	10489.4
		309	Divided	1.11345
		418	Subtracted	319.7	High confidence	10866.3	11186
		421	Divided	1.02942
	Squared	279	Subtracted	108.26		3670.49	3778.75
		444	Divided	1.02949
		602	Subtracted	91.53	Low confidence	2700.46	2791.99
		709	Divided	1.03389
	Rooted	333	Subtracted	2.3937		26.6816	29.0753
		381	Divided	1.08971
		405	Subtracted	0.7178	High confidence	32.9629	32.2451
		447	Divided	1.02226
alpha-amylase, salivary precursor (ec 3.2.1.1) (1,4-alpha-d-glucan glucanohydrolase). [swissprot;acc:p04745]	Measured	430	Subtracted	103.56	Low confidence	2105.24	2208.8
		432		103.26		2308.49	2205.23
		566	Divided	1.04919		2105.24	2208.8
		571		1.04683		2308.49	2205.23
	Ranked	122	Subtracted	1877.4		13113.5	11236.1
		133	Divided	1.16709
		331	Subtracted	818.61		10670.2	9851.59
		392	Divided	1.08309
	Squared	171	Subtracted	1312.68		11288.3	9975.62
		354	Divided	1.13159

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.