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

Results: HTML CSV LaTeX

Showing element 1825 to 1874 of 2060 in total

Network Comparison Type  : Subtracted
Interaction Map  : High confidence
Filtered  : 1
red  : 0
green  : 0
network_comparison  : 0

Rank	description	Hugo	Value Type
3212	rala binding protein 1; rala-binding protein. [refseq;acc:nm_006788]	RALBP1	Measured
			Ranked
			Squared
			Rooted
3213	malate dehydrogenase, cytoplasmic (ec 1.1.1.37). [swissprot;acc:p40925]	MDH1	Measured
			Ranked
			Squared
			Rooted
3214	bs4 protein (ny-ren-18 antigen). [swissprot;acc:q9y5a7]	NUB1	Measured
			Ranked
			Squared
			Rooted
3215	membrane-bound transcription factor site 2 protease (ec 3.4.24.-) (site-2 protease) (sterol-regulatory element-binding proteins intramembrane protease). [swissprot;acc:o43462]	MBTPS2	Measured
			Ranked
			Squared
			Rooted
3216	dna excision repair protein ercc-1. [swissprot;acc:p07992]	ERCC1	Measured
			Ranked
			Squared
			Rooted
3217	sex comb on midleg homolog 1. [refseq;acc:nm_012236]	SCMH1	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]	MLXIPL	Measured
			Ranked
			Squared
			Rooted
3219	protein c6orf55 (dopamine responsive protein drg-1) (my012 protein) (hspc228). [swissprot;acc:q9np79]	VTA1	Measured
			Ranked
			Squared
			Rooted
3220	transcription factor ap-2 beta (ap2-beta) (activating enhancer-binding protein 2 beta). [swissprot;acc:q92481]	TFAP2B	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]	PAFAH1B1	Measured
			Ranked
			Squared
			Rooted
3222	aldehyde dehydrogenase 7 (ec 1.2.1.5). [swissprot;acc:p43353]	ALDH3B1	Measured
			Ranked
			Squared
			Rooted
3223	ras-related protein ral-a. [swissprot;acc:p11233]	RALA	Measured
			Ranked
			Squared
			Rooted
3224	integrin alpha-3 precursor (galactoprotein b3) (gapb3) (vla-3 alpha chain) (cd49c). [swissprot;acc:p26006]	ITGA3	Measured
			Ranked

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
- Hugo is the HGNC identifier if it exists
- 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.