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	Interaction Map	Network Comparison Type	Filtered	red	green	network_comparison

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Showing element 12864 to 12912 of 12912 in total

Interaction Map  : High confidence
Network Comparison Type  : Divided
Filtered  : 1
red  : 0.00001
green  : 0.00001
network_comparison  : 1

Rank	description	Value Type
3216	dna excision repair protein ercc-1. [swissprot;acc:p07992]	Rooted
3217	sex comb on midleg homolog 1. [refseq;acc:nm_012236]	Measured
		Ranked
		Squared
		Rooted
3218	williams-beuren syndrome chromosome region 14 protein (ws basic-helix- loop-helix leucine zipper protein) (ws-bhlh) (mlx interactor). [swissprot;acc:q9np71]	Measured
		Ranked
		Squared
		Rooted
3219	protein c6orf55 (dopamine responsive protein drg-1) (my012 protein) (hspc228). [swissprot;acc:q9np79]	Measured
		Ranked
		Squared
		Rooted
3220	transcription factor ap-2 beta (ap2-beta) (activating enhancer-binding protein 2 beta). [swissprot;acc:q92481]	Measured
		Ranked
		Squared
		Rooted
3221	platelet-activating factor acetylhydrolase ib alpha subunit (ec 3.1.1.47) (paf acetylhydrolase 45 kda subunit) (paf-ah 45 kda subunit) (paf-ah alpha) (pafah alpha) (lissencephaly-1 protein) (lis- 1). [swissprot;acc:p43034]	Measured
		Ranked
		Squared
		Rooted
3222	aldehyde dehydrogenase 7 (ec 1.2.1.5). [swissprot;acc:p43353]	Measured
		Ranked
		Squared
		Rooted
3223	ras-related protein ral-a. [swissprot;acc:p11233]	Measured
		Ranked
		Squared
		Rooted
3224	integrin alpha-3 precursor (galactoprotein b3) (gapb3) (vla-3 alpha chain) (cd49c). [swissprot;acc:p26006]	Measured
		Ranked
		Squared
		Rooted
3225	heat-shock 20 kda like-protein p20. [swissprot;acc:o14558]	Measured
		Ranked
		Squared
		Rooted
3226	ccr4-not transcription complex, subunit 7 (ccr4-associated factor 1) (caf1) (btg1 binding factor 1). [swissprot;acc:q9uiv1]	Measured
		Ranked
		Squared
		Rooted
3227	69 kda islet cell autoantigen (ica69) (islet cell autoantigen 1) (islet cell autoantigen p69) (icap69). [swissprot;acc:q05084]	Measured
		Ranked
		Squared
		Rooted
3228	ezrin-binding partner pace-1 isoform 1. [refseq;acc:nm_020423]	Measured
		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.