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 1530 to 1579 of 1942 in total

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

Rank	description	Value Type
3125	gdp-fucose protein o-fucosyltransferase 1 precursor (ec 2.4.1.221) (peptide o-fucosyltransferase) (o-fuct-1). [swissprot;acc:q9h488]	Rooted
3126	1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta 4 (ec 3.1.4.11) (phosphoinositide phospholipase c) (plc-beta-4) (phospholipase c-beta-4). [swissprot;acc:q15147]	Measured
		Ranked
		Squared
		Rooted
3127	protein transport protein sec23b (sec23-related protein b). [swissprot;acc:q15437]	Measured
		Ranked
		Squared
		Rooted
3128	bone morphogenetic protein 7 precursor (bmp-7) (osteogenic protein 1) (op-1). [swissprot;acc:p18075]	Measured
		Ranked
		Squared
		Rooted
3129	cleavage stimulation factor, 50 kda subunit (cstf 50 kda subunit) (cf-1 50 kda subunit). [swissprot;acc:q05048]	Measured
		Ranked
		Squared
		Rooted
3130	prefoldin subunit 4 (protein c-1). [swissprot;acc:q9nqp4]	Measured
		Ranked
		Squared
		Rooted
3131	protein c20orf24 (rab5-interacting protein) (rip5) (pnas-11). [swissprot;acc:q9buv8]	Measured
		Ranked
		Squared
		Rooted
3132	r3h domain (binds single-stranded nucleic acids) containing-like. [refseq;acc:nm_178491]	Measured
		Ranked
		Squared
		Rooted
3133	ngd5 protein homolog (cgi-53). [swissprot;acc:q9y366]	Measured
		Ranked
		Squared
		Rooted
3134	rab geranylgeranyltransferase alpha subunit (ec 2.5.1.-) (rab geranyl- geranyltransferase alpha subunit) (rab gg transferase alpha) (rab ggtase alpha). [swissprot;acc:q92696]	Measured
		Ranked
		Squared
		Rooted
3135	protein transport protein sec23a (sec23-related protein a). [swissprot;acc:q15436]	Measured
		Ranked
		Squared
		Rooted
3136	vaccinia related kinase 1; vaccinia-related kinase-1. [refseq;acc:nm_003384]	Measured
		Ranked
		Squared
		Rooted
3137	serine/threonine-protein kinase kkialre (ec 2.7.1.-) (cyclin-dependent kinase-like 1). [swissprot;acc:q00532]	Measured
		Ranked
		Squared
		Rooted
3138	hcdi protein. [refseq;acc:nm_020195]	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.