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

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Showing element 6041 to 6090 of 6456 in total

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

Rank	description	Network Comparison Type	red	green	network_comparison
3021	testis-specific protein tpx-1 precursor (cysteine-rich secretory protein-2) (crisp-2). [swissprot;acc:p16562]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3022	n-acetylglucosamine kinase (ec 2.7.1.59) (glcnac kinase). [swissprot;acc:q9uj70]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3023	vesicle-associated membrane protein-associated protein b/c (vamp- associated protein b/c) (vamp-b/vamp-c) (vap-b/vap-c). [swissprot;acc:o95292]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3024	phosphatidylinositol glycan class t precursor. [refseq;acc:nm_015937]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3025	dj579f20.1 (high-mobility group (nonhistone chromosomal) protein 1-like 1). [sptrembl;acc:q9nqj4]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3026	solute carrier family 36 member 1; proton / amino acid symporter; lysosomal amino acid transporter 1. [refseq;acc:nm_078483]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3027	elongation factor ts, mitochondrial precursor (ef-ts) (ef-tsmt). [swissprot;acc:p43897]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3028	clll6 protein. [refseq;acc:nm_020456]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3029	dynein intermediate chain 1, axonemal (axonemal dynein intermediate chain 1). [swissprot;acc:q9ui46]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3030	uncharacterized bone marrow protein bm033. [refseq;acc:nm_018452]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3031	speckle-type poz protein. [swissprot;acc:o43791]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3032	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3033	glycerol-3-phosphate acyltransferase, mitochondrial precursor (ec 2.3.1.15) (gpat). [swissprot;acc:q9hcl2]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3034	postsynaptic protein cript; hspc139 protein. [refseq;acc:nm_014171]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3035	transforming growth factor beta 3 precursor (tgf-beta 3). [swissprot;acc:p10600]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3036	placenta growth factor precursor (plgf). [swissprot;acc:p49763]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3037	skd1 protein (vacuolar sorting protein 4b). [swissprot;acc:o75351]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3038	spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [swissprot;acc:q13813]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3039	set protein (hla-dr associated protein ii) (phapii) (phosphatase 2a inhibitor i2pp2a). [swissprot;acc:q01105]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3040	connective tissue growth factor precursor (hypertrophic chondrocyte- specific protein 24). [swissprot;acc:p29279]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3041	transthyretin precursor (prealbumin) (tbpa) (ttr) (attr). [swissprot;acc:p02766]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3042	orphan nuclear receptor nr5a2 (alpha-1-fetoprotein transcription factor) (hepatocytic transcription factor) (b1-binding factor) (hb1f) (cyp7a promoter binding factor). [swissprot;acc:o00482]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3043	transcription termination factor, rna polymerase ii; lodestar protein. [refseq;acc:nm_003594]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3044	late endosomal/lysosomal mp1 interacting protein (p14) (hspc003). [swissprot;acc:q9y2q5]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3045	dna mismatch repair protein msh6 (muts-alpha 160 kda subunit) (g/t mismatch binding protein) (gtbp) (gtmbp) (p160). [swissprot;acc:p52701]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0

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.