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 6212 to 6261 of 6456 in total

Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Network Comparison Type	red	green	network_comparison
3106	prostate tumor overexpressed gene 1; prostate tumor over expressed gene 1. [refseq;acc:nm_017432]	Subtracted	0	0	0
3107	lyl-1 protein (lymphoblastic leukemia derived sequence 1). [swissprot;acc:p12980]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3108	sorting nexin 16. [swissprot;acc:p57768]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3109	wnt1 inducible signaling pathway protein 1 isoform 1 precursor; wnt-1 signaling pathway protein 1; wnt1 signaling pathway protein 1; wnt-1 inducible signaling pathway protein 1. [refseq;acc:nm_003882]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3110	ras-related protein rab-2a. [swissprot;acc:p08886]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3111	serine/threonine protein kinase 3 (ec 2.7.1.37) (ste20-like kinase mst2) (mst-2) (mammalian ste20-like protein kinase 2) (serine/threonine protein kinase krs-1). [swissprot;acc:q13188]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3112	ras-related protein rab-11a (rab-11) (24kg) (yl8). [swissprot;acc:p24410]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3113	nuclear transport factor 2 (ntf-2) (placental protein 15) (pp15). [swissprot;acc:p13662]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3114	regulatory protein tsc-22 (tgfb stimulated clone 22 homolog). [swissprot;acc:q15714]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3115	serine/threonine protein kinase 24 (ec 2.7.1.37) (ste20-like kinase mst3) (mst-3) (mammalian ste20-like protein kinase 3). [swissprot;acc:q9y6e0]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3116	mo25-like protein. [swissprot;acc:q9h9s4]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3117	ba203i16.1 (hypothetical protein kiaa0970). [sptrembl;acc:q9h1w1]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3118	spermine synthase (ec 2.5.1.22) (spermidine aminopropyltransferase) (spmsy). [swissprot;acc:p52788]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3119	rab gdp dissociation inhibitor alpha (rab gdi alpha) (gdi-1) (xap-4) (oligophrenin 2). [swissprot;acc:p31150]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3120	sex comb on midleg-like 2; sex comb on midleg like 2. [refseq;acc:nm_006089]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3121	glycine receptor alpha-2 chain precursor. [swissprot;acc:p23416]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3122	ribose-phosphate pyrophosphokinase ii (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase ii) (ppribp) (prs-ii). [swissprot;acc:p11908]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3123	vesicle-associated membrane protein-associated protein a (vamp- associated protein a) (vamp-a) (vap-a) (33 kda vamp-associated protein) (vap-33). [swissprot;acc:q9p0l0]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3124	sam domain and hd domain-containing protein 1 (dendritic cell-derived ifng-induced protein) (dcip) (monocyte protein 5) (mop-5). [swissprot;acc:q9y3z3]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3125	gdp-fucose protein o-fucosyltransferase 1 precursor (ec 2.4.1.221) (peptide o-fucosyltransferase) (o-fuct-1). [swissprot;acc:q9h488]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
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]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3127	protein transport protein sec23b (sec23-related protein b). [swissprot;acc:q15437]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3128	bone morphogenetic protein 7 precursor (bmp-7) (osteogenic protein 1) (op-1). [swissprot;acc:p18075]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3129	cleavage stimulation factor, 50 kda subunit (cstf 50 kda subunit) (cf-1 50 kda subunit). [swissprot;acc:q05048]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3130	prefoldin subunit 4 (protein c-1). [swissprot;acc:q9nqp4]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3131	protein c20orf24 (rab5-interacting protein) (rip5) (pnas-11). [swissprot;acc:q9buv8]	Divided	0.00001	0.00001	1

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.