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 12714 to 12763 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
3179	carcinoma related gene. [refseq;acc:nm_016041]	Ranked
		Squared
		Rooted
3180	3-hydroxyacyl-coa dehydrogenase type ii (ec 1.1.1.35) (type ii hadh) (endoplasmic reticulum-associated amyloid beta-peptide binding protein) (short-chain type dehydrogenase/reductase xh98g2). [swissprot;acc:q99714]	Measured
		Ranked
		Squared
		Rooted
3181	fatty aldehyde dehydrogenase (ec 1.2.1.3) (aldehyde dehydrogenase, microsomal) (aldh class 3). [swissprot;acc:p51648]	Measured
		Ranked
		Squared
		Rooted
3182	transcription factor e2-alpha (immunoglobulin enhancer binding factor e12/e47) (transcription factor-3) (tcf-3) (immunoglobulin transcription factor-1) (transcription factor itf-1) (kappa-e2-binding factor). [swissprot;acc:p15923]	Measured
		Ranked
		Squared
		Rooted
3183	core-binding factor, beta subunit (cbf-beta) (polyomavirus enhancer binding protein 2 beta subunit) (pebp2-beta) (pea2-beta) (sl3-3 enhancer factor 1 beta subunit) (sl3/akv core-binding factor beta subunit). [swissprot;acc:q13951]	Measured
		Ranked
		Squared
		Rooted
3184	nuclear autoantigen sp-100 (speckled 100 kda) (nuclear dot-associated sp100 protein) (lysp100b). [swissprot;acc:p23497]	Measured
		Ranked
		Squared
		Rooted
3185	ferrochelatase, mitochondrial precursor (ec 4.99.1.1) (protoheme ferro-lyase) (heme synthetase). [swissprot;acc:p22830]	Measured
		Ranked
		Squared
		Rooted
3186	protein kinase c, theta type (ec 2.7.1.-) (npkc-theta). [swissprot;acc:q04759]	Measured
		Ranked
		Squared
		Rooted
3187	doublesex and mab-3 related transcription factor 3; testis-specific protein; dmrt-like family a3. [refseq;acc:nm_021240]	Measured
		Ranked
		Squared
		Rooted
3188	connective tissue growth factor-like protein precursor (ctgf-l) (wnt1 inducible signaling pathway protein 2) (wisp-2) (connective tissue growth factor-related protein 58). [swissprot;acc:o76076]	Measured
		Ranked
		Squared
		Rooted
3189	ring finger protein 4. [swissprot;acc:p78317]	Measured
		Ranked
		Squared
		Rooted
3190	myotubularin-related protein 1 (ec 3.1.3.-). [swissprot;acc:q13613]	Measured
		Ranked
		Squared
		Rooted
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]	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.