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

Results: HTML CSV LaTeX

Showing element 25726 to 25775 of 25824 in total

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

Rank	description	Value Type
3204	vaccinia related kinase 2; vaccinia-related kinase-2. [refseq;acc:nm_006296]	Ranked
		Squared
		Rooted
3205	rb1-inducible coiled coil protein 1. [refseq;acc:nm_014781]	Measured
		Ranked
		Squared
		Rooted
3206	protein c20orf43 (hspc164/hspc169) (ad-007) (cda05). [swissprot;acc:q9by42]	Measured
		Ranked
		Squared
		Rooted
3207	complement component c8 beta chain precursor. [swissprot;acc:p07358]	Measured
		Ranked
		Squared
		Rooted
3208	runt-related transcription factor 3 (core-binding factor, alpha 3 subunit) (cbf-alpha 3) (acute myeloid leukemia 2 protein) (oncogene aml-2) (polyomavirus enhancer binding protein 2 alpha c subunit) (pebp2-alpha c) (pea2-alpha c) (sl3-3 enhancer factor 1 alpha c subunit) (sl3/akv core-binding factor alpha c subunit). [swissprot;acc:q13761]	Measured
		Ranked
		Squared
		Rooted
3209	cdk-activating kinase assembly factor mat1 (ring finger protein mat1) (menage a trois) (cdk7/cyclin h assembly factor) (p36) (p35) (cyclin g1 interacting protein). [swissprot;acc:p51948]	Measured
		Ranked
		Squared
		Rooted
3210	trabid protein. [swissprot;acc:q9ugi0]	Measured
		Ranked
		Squared
		Rooted
3211	cytochrome p450 24a1, mitochondrial precursor (ec 1.14.-.-) (p450- cc24) (vitamin d(3) 24-hydroxylase) (1,25-dihydroxyvitamin d(3) 24- hydroxylase) (24-ohase). [swissprot;acc:q07973]	Measured
		Ranked
		Squared
		Rooted
3212	rala binding protein 1; rala-binding protein. [refseq;acc:nm_006788]	Measured
		Ranked
		Squared
		Rooted
3213	malate dehydrogenase, cytoplasmic (ec 1.1.1.37). [swissprot;acc:p40925]	Measured
		Ranked
		Squared
		Rooted
3214	bs4 protein (ny-ren-18 antigen). [swissprot;acc:q9y5a7]	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]	Measured
		Ranked
		Squared
		Rooted
3216	dna excision repair protein ercc-1. [swissprot;acc:p07992]	Measured
		Ranked
		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
- 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.