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

Results: HTML CSV LaTeX

Showing element 1136 to 1185 of 1892 in total

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

Rank	Hugo	Value Type	description
3039	SET	Rooted	set protein (hla-dr associated protein ii) (phapii) (phosphatase 2a inhibitor i2pp2a). [swissprot;acc:q01105]
3040	CTGF	Measured	connective tissue growth factor precursor (hypertrophic chondrocyte- specific protein 24). [swissprot;acc:p29279]
		Ranked
		Squared
		Rooted
3041	TTR	Measured	transthyretin precursor (prealbumin) (tbpa) (ttr) (attr). [swissprot;acc:p02766]
		Ranked
		Squared
		Rooted
3042	NR5A2	Measured	orphan nuclear receptor nr5a2 (alpha-1-fetoprotein transcription factor) (hepatocytic transcription factor) (b1-binding factor) (hb1f) (cyp7a promoter binding factor). [swissprot;acc:o00482]
		Ranked
		Squared
		Rooted
3043	TTF2	Measured	transcription termination factor, rna polymerase ii; lodestar protein. [refseq;acc:nm_003594]
		Ranked
		Squared
		Rooted
3044	no value	Measured	late endosomal/lysosomal mp1 interacting protein (p14) (hspc003). [swissprot;acc:q9y2q5]
		Ranked
		Squared
		Rooted
3045	MSH6	Measured	dna mismatch repair protein msh6 (muts-alpha 160 kda subunit) (g/t mismatch binding protein) (gtbp) (gtmbp) (p160). [swissprot;acc:p52701]
		Ranked
		Squared
		Rooted
3046	CD207	Measured	langerhans cell specific c-type lectin. [refseq;acc:nm_015717]
		Ranked
		Squared
		Rooted
3047	ORC2L	Measured	origin recognition complex subunit 2. [swissprot;acc:q13416]
		Ranked
		Squared
		Rooted
3048	STK25	Measured	serine/threonine protein kinase 25 (ec 2.7.1.37) (sterile 20/oxidant stress-response kinase 1) (ste20/oxidant stress response kinase-1) (sok-1) (ste20-like kinase). [swissprot;acc:o00506]
		Ranked
		Squared
		Rooted
3049	SLC30A3	Measured	zinc transporter 3 (znt-3). [swissprot;acc:q99726]
		Ranked
		Squared
		Rooted
3050	ACVR1	Measured	activin receptor type i precursor (ec 2.7.1.37) (actr-i) (serine/threonine-protein kinase receptor r1) (skr1) (activin receptor-like kinase 2) (alk-2) (tgf-b superfamily receptor type i) (tsr-i). [swissprot;acc:q04771]
		Ranked
		Squared
		Rooted
3051	CYB561D2	Measured	putative tumor suppressor 101f6. [refseq;acc:nm_007022]
		Ranked
		Squared
		Rooted
3052	PDCD10	Measured	programmed cell death 10; apoptosis-related protein 15. [refseq;acc:nm_007217]

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.