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

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Showing element 501 to 515 of 515 in total

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

description	Rank	Hugo
vascular endothelial growth factor a precursor (vegf-a) (vascular permeability factor) (vpf). [swissprot;acc:p15692]	3066	VEGFA
vascular endothelial growth factor b precursor (vegf-b) (vegf related factor) (vrf). [swissprot;acc:p49765]	2811	VEGFB
vasopressin-activated calcium-mobilizing receptor (vacm-1) (cullin homolog 5) (cul-5). [swissprot;acc:q93034]	2840	CUL5
vesicle transport-related protein isoform a; vesicle transport-related protein. [refseq;acc:nm_016106]	3157	SCFD1
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]	3123	VAPA
vesicle-associated membrane protein-associated protein b/c (vamp- associated protein b/c) (vamp-b/vamp-c) (vap-b/vap-c). [swissprot;acc:o95292]	3023	VAPB
vps28 protein homolog. [swissprot;acc:q9uk41]	2871	VPS28
wd-repeat containing protein ciao 1. [swissprot;acc:o76071]	2927	CIAO1
williams-beuren syndrome chromosome region 14 protein (ws basic-helix- loop-helix leucine zipper protein) (ws-bhlh) (mlx interactor). [swissprot;acc:q9np71]	3218	MLXIPL
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]	3109	WISP1
wnt1 inducible signaling pathway protein 3 isoform 1; wnt-1 signaling pathway protein 3; wnt1 signaling pathway protein 3; wnt-1 inducible signaling pathway protein 3. [refseq;acc:nm_003880]	3065	WISP3
xanthine dehydrogenase/oxidase [includes: xanthine dehydrogenase (ec 1.1.1.204) (xd); xanthine oxidase (ec 1.1.3.22) (xo) (xanthine oxidoreductase)]. [swissprot;acc:p47989]	2882	XDH
zinc finger daz interacting protein 1. [refseq;acc:nm_014934]	2981	DZIP1
zinc transporter 1 (znt-1). [swissprot;acc:q9y6m5]	2822	SLC30A1
zinc transporter 3 (znt-3). [swissprot;acc:q99726]	3049	SLC30A3

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
- Hugo is the HGNC identifier if it exists
- 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.