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

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Showing element 25776 to 25824 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

Rank	description	Value Type	Network Comparison Type	red	green	network_comparison
3222	aldehyde dehydrogenase 7 (ec 1.2.1.5). [swissprot;acc:p43353]	Rooted	Subtracted	0	0	0
3223	ras-related protein ral-a. [swissprot;acc:p11233]	Measured	Divided	0.00001	0.00001	1
			Subtracted	0	0	0
		Ranked	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
3224	integrin alpha-3 precursor (galactoprotein b3) (gapb3) (vla-3 alpha chain) (cd49c). [swissprot;acc:p26006]	Measured	Divided	0.00001	0.00001	1
			Subtracted	0	0	0
		Ranked	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
3225	heat-shock 20 kda like-protein p20. [swissprot;acc:o14558]	Measured	Divided	0.00001	0.00001	1
			Subtracted	0	0	0
		Ranked	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
3226	ccr4-not transcription complex, subunit 7 (ccr4-associated factor 1) (caf1) (btg1 binding factor 1). [swissprot;acc:q9uiv1]	Measured	Divided	0.00001	0.00001	1
			Subtracted	0	0	0
		Ranked	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
3227	69 kda islet cell autoantigen (ica69) (islet cell autoantigen 1) (islet cell autoantigen p69) (icap69). [swissprot;acc:q05084]	Measured	Divided	0.00001	0.00001	1
			Subtracted	0	0	0
		Ranked	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
3228	ezrin-binding partner pace-1 isoform 1. [refseq;acc:nm_020423]	Measured	Divided	0.00001	0.00001	1
			Subtracted	0	0	0
		Ranked	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

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.