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	Network Comparison Type	Interaction Map	Filtered	red	green	network_comparison

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Showing element 12164 to 12213 of 12912 in total

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

Rank	description	Value Type
3041	transthyretin precursor (prealbumin) (tbpa) (ttr) (attr). [swissprot;acc:p02766]	Rooted
3042	orphan nuclear receptor nr5a2 (alpha-1-fetoprotein transcription factor) (hepatocytic transcription factor) (b1-binding factor) (hb1f) (cyp7a promoter binding factor). [swissprot;acc:o00482]	Measured
		Ranked
		Squared
		Rooted
3043	transcription termination factor, rna polymerase ii; lodestar protein. [refseq;acc:nm_003594]	Measured
		Ranked
		Squared
		Rooted
3044	late endosomal/lysosomal mp1 interacting protein (p14) (hspc003). [swissprot;acc:q9y2q5]	Measured
		Ranked
		Squared
		Rooted
3045	dna mismatch repair protein msh6 (muts-alpha 160 kda subunit) (g/t mismatch binding protein) (gtbp) (gtmbp) (p160). [swissprot;acc:p52701]	Measured
		Ranked
		Squared
		Rooted
3046	langerhans cell specific c-type lectin. [refseq;acc:nm_015717]	Measured
		Ranked
		Squared
		Rooted
3047	origin recognition complex subunit 2. [swissprot;acc:q13416]	Measured
		Ranked
		Squared
		Rooted
3048	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]	Measured
		Ranked
		Squared
		Rooted
3049	zinc transporter 3 (znt-3). [swissprot;acc:q99726]	Measured
		Ranked
		Squared
		Rooted
3050	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]	Measured
		Ranked
		Squared
		Rooted
3051	putative tumor suppressor 101f6. [refseq;acc:nm_007022]	Measured
		Ranked
		Squared
		Rooted
3052	programmed cell death 10; apoptosis-related protein 15. [refseq;acc:nm_007217]	Measured
		Ranked
		Squared
		Rooted
3053	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]	Measured
		Ranked
		Squared
		Rooted
3054	double-stranded rna-binding zinc finger protein jaz. [refseq;acc:nm_012279]	Measured

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.