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 1951 to 2000 of 2060 in total

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

Rank	description	Hugo	Value Type
5034	rap1 gtpase-gdp dissociation stimulator 1 (smg p21 stimulatory gdp/gtp exchange protein) (smg gds protein) (exchange factor smggds). [swissprot;acc:p52306]	RAP1GDS1	Squared
			Rooted
	solute carrier family 21 member 15 (organic anion transporter polypeptide-related protein 4) (oatp-rp4) (oatprp4). [swissprot;acc:q9h2y9]	SLCO5A1	Ranked
5035	lipin 1. [swissprot;acc:q14693]	LPIN1
	solute carrier family 21 member 15 (organic anion transporter polypeptide-related protein 4) (oatp-rp4) (oatprp4). [swissprot;acc:q9h2y9]	SLCO5A1	Measured
			Squared
			Rooted
5036	lipin 1. [swissprot;acc:q14693]	LPIN1	Measured
			Squared
			Rooted
	lipin 3 (lipin 3-like) (fragments). [swissprot;acc:q9bqk8]	LPIN3	Ranked
5037			Measured
			Squared
			Rooted
	myeloblast kiaa0230 (fragment). [sptrembl;acc:q92626]	PXDN	Ranked
5038			Measured
			Squared
			Rooted
	testis specific leucine rich repeat protein. [refseq;acc:nm_012472]	LRRC6	Ranked
5039	major centromere autoantigen b (centromere protein b) (cenp-b). [swissprot;acc:p07199]	CENPB
	testis specific leucine rich repeat protein. [refseq;acc:nm_012472]	LRRC6	Measured
			Squared
			Rooted
5040	leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735]	LRRFIP1	Ranked
	major centromere autoantigen b (centromere protein b) (cenp-b). [swissprot;acc:p07199]	CENPB	Measured
			Squared
			Rooted
5041	leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735]	LRRFIP1	Measured
			Squared
			Rooted
	n-acetylglucosamine kinase (ec 2.7.1.59) (glcnac kinase). [swissprot;acc:q9uj70]	NAGK	Ranked
5042			Measured
			Squared
			Rooted
	transthyretin precursor (prealbumin) (tbpa) (ttr) (attr). [swissprot;acc:p02766]	TTR	Ranked
5043	late endosomal/lysosomal mp1 interacting protein (p14) (hspc003). [swissprot;acc:q9y2q5]	no value
	transthyretin precursor (prealbumin) (tbpa) (ttr) (attr). [swissprot;acc:p02766]	TTR	Measured
			Squared
			Rooted
5044	langerhans cell specific c-type lectin. [refseq;acc:nm_015717]	CD207	Ranked
	late endosomal/lysosomal mp1 interacting protein (p14) (hspc003). [swissprot;acc:q9y2q5]	no value	Measured
			Squared
			Rooted
5045	langerhans cell specific c-type lectin. [refseq;acc:nm_015717]	CD207	Measured
			Squared
			Rooted
	putative tumor suppressor 101f6. [refseq;acc:nm_007022]	CYB561D2	Ranked
5046	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]	HGD
	putative tumor suppressor 101f6. [refseq;acc:nm_007022]	CYB561D2	Measured
			Squared

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.