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	Gene	green	Interaction Map	Network Comparison Type	Filtered	network_comparison	red

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Showing element 3180 to 3229 of 66312 in total

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description	Rank	Value Type	green	Interaction Map	Network Comparison Type	network_comparison	red
actin binding lim protein 2. [refseq;acc:nm_032432]	1937	Squared	30386.4	High confidence	Subtracted	2122	28264.4
	2127	Measured	7921.78	Low confidence		251.78	7670
	2332	Squared	30386.4	High confidence	Divided	1.07508	28264.4
	3513		42371.9	Low confidence		1.03234	43742.1
	3597				Subtracted	1370.2
actin, alpha cardiac. [swissprot;acc:p04270]	914		43771.9			2123.1	45895
	966				Divided	1.0485
	3923	Rooted	74.3873		Subtracted	2.0033	72.384
	3960				Divided	1.02768
	3962	Ranked	198.479			1.01209	200.879
	3973				Subtracted	2.4
	4021	Measured	8251.68		Divided	1.02213	8073.06
	4148				Subtracted	178.62
actin, aortic smooth muscle (alpha-actin 2). [swissprot;acc:p03996]	917	Squared	43772			2122.9	45894.9
	967				Divided	1.0485
	3924	Rooted	74.3879		Subtracted	2.0033	72.3846
	3961				Divided	1.02768
	3964	Ranked	198.477			1.01209	200.877
	3974				Subtracted	2.4
	4022	Measured	8251.74		Divided	1.02213	8073.12
	4149				Subtracted	178.62
actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571]	1206	Squared	31619.6	High confidence		3064.8	28554.8
	1280	Measured	6512.64			476.42	6036.22
	1284	Rooted	65.7244			2.7188	63.0056
	1307				Divided	1.04315
	1354	Measured	6512.64			1.07893	6036.22
	1529	Ranked	213.031			1.01751	216.762
	1536				Subtracted	3.731
	1636	Squared	31619.6		Divided	1.10733	28554.8
	1671		43374.8	Low confidence		1.04246	45216.3
	1737				Subtracted	1841.5
	3385	Measured	8213.1			211.21	8001.89
	3418				Divided	1.0264
	3425	Rooted	74.3776		Subtracted	2.1954	72.1822
	3454				Divided	1.03041
	3630	Ranked	197.828			1.01418	200.633
	3638				Subtracted	2.805
actin, gamma-enteric smooth muscle (alpha-actin 3). [swissprot;acc:p12718]	916	Squared	43772			2122.9	45894.9
	965				Divided	1.0485
	3922	Rooted	74.3879		Subtracted	2.0033	72.3846
	3959				Divided	1.02768
	3961	Ranked	198.477			1.01209	200.877
	3972				Subtracted	2.4
	4020	Measured	8251.74		Divided	1.02213	8073.12
	4147				Subtracted	178.62
actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [refseq;acc:nm_002313]	629	Rooted	64.7371	High confidence		4.7242	60.0129
	633	Ranked	216.576			12.496	229.072
	640	Rooted	64.7371		Divided	1.07872	60.0129
	668	Ranked	216.576			1.0577	229.072
	776		203.181	Low confidence	Subtracted	5.307	208.488

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.