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.

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

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

Results: HTML CSV LaTeX

Showing element 1930 to 1979 of 2060 in total

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

Rank	Hugo	Value Type	description
5029	CLEC4F	Measured	likely ortholog of mouse c-type (calcium dependent, carbohydrate recognition domain) lectin, superfamily member 13; c-type lectin 13; likely ortholog of rat kupffer cell c-type lectin receptor. [refseq;acc:nm_173535]
		Squared
		Rooted
	GGTLA4	Ranked	gamma-glutamyltransferase-like activity 4; gamma-glutamyltranspeptidase-like. [refseq;acc:nm_080920]
5030	CBWD1		cobw-like protein. [refseq;acc:nm_018491]
	GGTLA4	Measured	gamma-glutamyltransferase-like activity 4; gamma-glutamyltranspeptidase-like. [refseq;acc:nm_080920]
		Squared
		Rooted
5031	CBWD1	Measured	cobw-like protein. [refseq;acc:nm_018491]
		Squared
		Rooted
	TIGD7	Ranked	tigger transposable element derived 7; jerky (mouse) homolog-like. [refseq;acc:nm_033208]
5032	SRP14		signal recognition particle 14 kda protein (srp14) (18 kda alu rna binding protein). [swissprot;acc:p37108]
	TIGD7	Measured	tigger transposable element derived 7; jerky (mouse) homolog-like. [refseq;acc:nm_033208]
		Squared
		Rooted
5033	RAP1GDS1	Ranked	rap1 gtpase-gdp dissociation stimulator 1 (smg p21 stimulatory gdp/gtp exchange protein) (smg gds protein) (exchange factor smggds). [swissprot;acc:p52306]
	SRP14	Measured	signal recognition particle 14 kda protein (srp14) (18 kda alu rna binding protein). [swissprot;acc:p37108]
		Squared
		Rooted
5034	RAP1GDS1	Measured	rap1 gtpase-gdp dissociation stimulator 1 (smg p21 stimulatory gdp/gtp exchange protein) (smg gds protein) (exchange factor smggds). [swissprot;acc:p52306]
		Squared
		Rooted
	SLCO5A1	Ranked	solute carrier family 21 member 15 (organic anion transporter polypeptide-related protein 4) (oatp-rp4) (oatprp4). [swissprot;acc:q9h2y9]
5035	LPIN1		lipin 1. [swissprot;acc:q14693]
	SLCO5A1	Measured	solute carrier family 21 member 15 (organic anion transporter polypeptide-related protein 4) (oatp-rp4) (oatprp4). [swissprot;acc:q9h2y9]
		Squared
		Rooted
5036	LPIN1	Measured	lipin 1. [swissprot;acc:q14693]
		Squared
		Rooted
	LPIN3	Ranked	lipin 3 (lipin 3-like) (fragments). [swissprot;acc:q9bqk8]
5037		Measured
		Squared
		Rooted
	PXDN	Ranked	myeloblast kiaa0230 (fragment). [sptrembl;acc:q92626]
5038	LRRC6		testis specific leucine rich repeat protein. [refseq;acc:nm_012472]
	PXDN	Measured	myeloblast kiaa0230 (fragment). [sptrembl;acc:q92626]
		Squared
		Rooted
5039	CENPB	Ranked	major centromere autoantigen b (centromere protein b) (cenp-b). [swissprot;acc:p07199]
	LRRC6	Measured	testis specific leucine rich repeat protein. [refseq;acc:nm_012472]
		Squared
		Rooted
5040	CENPB	Measured	major centromere autoantigen b (centromere protein b) (cenp-b). [swissprot;acc:p07199]
		Squared
		Rooted
	LRRFIP1	Ranked	leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735]
5041		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.