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

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Showing element 3180 to 3229 of 77072 in total

green  : 0.00001
red  : 0.00001
network_comparison  : 1
Filtered  : 1
Network Comparison Type  : Divided

description	Value Type	Rank	Interaction Map
myosin heavy chain, nonmuscle type a (cellular myosin heavy chain, type a) (nonmuscle myosin heavy chain-a) (nmmhc-a). [swissprot;acc:p35579]	Squared	3140	High confidence
	Rooted
myosin heavy chain, nonmuscle type b (cellular myosin heavy chain, type b) (nonmuscle myosin heavy chain-b) (nmmhc-b). [swissprot;acc:p35580]	Measured	2988
	Ranked
	Squared
	Rooted
myosin heavy chain, smooth muscle isoform (smmhc). [swissprot;acc:p35749]	Measured	2985
	Ranked
	Squared
	Rooted
myotubularin-related protein 1 (ec 3.1.3.-). [swissprot;acc:q13613]	Measured	3190
	Ranked
	Squared
	Rooted
myotubularin-related protein 2 (ec 3.1.3.-). [swissprot;acc:q13614]	Measured	3166
	Ranked
	Squared
	Rooted
n-acetylglucosamine kinase (ec 2.7.1.59) (glcnac kinase). [swissprot;acc:q9uj70]	Measured	3022
		5042	Low confidence
	Ranked	3022	High confidence
		5041	Low confidence
	Squared	3022	High confidence
		5042	Low confidence
	Rooted	3022	High confidence
		5042	Low confidence
nadh-ubiquinone oxidoreductase 13 kda-b subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-b) (ci-13kd-b) (complex i subunit b13). [swissprot;acc:q16718]	Measured	3005	High confidence
	Ranked
	Squared
	Rooted
nadh-ubiquinone oxidoreductase 24 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3). [swissprot;acc:p19404]	Measured	2795
	Ranked
	Squared
	Rooted
nadh-ubiquinone oxidoreductase 30 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-30kd) (ci-30kd). [swissprot;acc:o75489]	Measured	3081
	Ranked
	Squared
	Rooted
nadh-ubiquinone oxidoreductase 39 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-39kd) (ci-39kd). [swissprot;acc:q16795]	Measured	2954
	Ranked
	Squared
	Rooted
nadh-ubiquinone oxidoreductase 49 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-49kd) (ci-49kd). [swissprot;acc:o75306]	Measured	2878
	Ranked
	Squared
	Rooted
nanos (fragment). [sptrembl;acc:q8wy41]	Measured	2803
	Ranked
	Squared
	Rooted

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.