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

Results: HTML CSV LaTeX

Showing element 12764 to 12813 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
3191	amyloid beta precursor protein-binding protein 2; amyloid beta precursor protein (cytoplasmic tail)-binding protein 2; protein interacting with app tail 1. [refseq;acc:nm_006380]	Rooted
3192	ubiquitin carboxyl-terminal hydrolase 13 (ec 3.1.2.15) (ubiquitin thiolesterase 13) (ubiquitin-specific processing protease 13) (deubiquitinating enzyme 13) (isopeptidase t-3) (isot-3). [swissprot;acc:q92995]	Measured
		Ranked
		Squared
		Rooted
3193	rab gdp dissociation inhibitor beta (rab gdi beta) (gdi-2). [swissprot;acc:p50395]	Measured
		Ranked
		Squared
		Rooted
3194	muts protein homolog 4. [swissprot;acc:o15457]	Measured
		Ranked
		Squared
		Rooted
3195	integrin beta-3 precursor (platelet membrane glycoprotein iiia) (gpiiia) (cd61 antigen). [swissprot;acc:p05106]	Measured
		Ranked
		Squared
		Rooted
3196	homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein (methyl methanesulfonate (mmf)-inducible fragment protein 1). [swissprot;acc:q15011]	Measured
		Ranked
		Squared
		Rooted
3197	cisplatin resistance related protein crr9p. [refseq;acc:nm_030782]	Measured
		Ranked
		Squared
		Rooted
3198	rp42 homolog; squamous cell carcinoma-related oncogene. [refseq;acc:nm_020640]	Measured
		Ranked
		Squared
		Rooted
3199	complement component c6 precursor. [swissprot;acc:p13671]	Measured
		Ranked
		Squared
		Rooted
3200	endosome-associated fyve-domain protein. [refseq;acc:nm_014733]	Measured
		Ranked
		Squared
		Rooted
3201	recessive polycystic kidney disease protein tg737 homolog. [swissprot;acc:q13099]	Measured
		Ranked
		Squared
		Rooted
3202	ran binding protein 3 isoform ranbp3-d; ran-binding protein-3. [refseq;acc:nm_007322]	Measured
		Ranked
		Squared
		Rooted
3203	high mobility group protein 4 (hmg-4) (high mobility group protein 2a) (hmg-2a). [swissprot;acc:o15347]	Measured
		Ranked
		Squared
		Rooted
3204	vaccinia related kinase 2; vaccinia-related kinase-2. [refseq;acc:nm_006296]	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.