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

Results: HTML CSV LaTeX

Showing element 1208 to 1257 of 2060 in total

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

Rank	Hugo	Value Type	description
3057	C9	Rooted	complement component c9 precursor. [swissprot;acc:p02748]
3058	GNPDA1	Measured	glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926]
		Ranked
		Squared
		Rooted
3059	RNASEN	Measured	ribonuclease iii (ec 3.1.26.3) (rnase iii) (p241). [swissprot;acc:q9nrr4]
		Ranked
		Squared
		Rooted
3060	TTC1	Measured	tetratricopeptide repeat protein 1 (tpr repeat protein 1). [swissprot;acc:q99614]
		Ranked
		Squared
		Rooted
3061	CNOT6	Measured	kiaa1194. [refseq;acc:nm_015455]
		Ranked
		Squared
		Rooted
3062	SPARC	Measured	sparc precursor (secreted protein acidic and rich in cysteine) (osteonectin) (on) (basement membrane protein bm-40). [swissprot;acc:p09486]
		Ranked
		Squared
		Rooted
3063	MRPS30	Measured	mitochondrial 28s ribosomal protein s30 (s30mt) (mrp-s30) (programmed cell death protein 9) (bm047). [swissprot;acc:q9np92]
		Ranked
		Squared
		Rooted
3064	C7	Measured	complement component c7 precursor. [swissprot;acc:p10643]
		Ranked
		Squared
		Rooted
3065	WISP3	Measured	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]
		Ranked
		Squared
		Rooted
3066	VEGFA	Measured	vascular endothelial growth factor a precursor (vegf-a) (vascular permeability factor) (vpf). [swissprot;acc:p15692]
		Ranked
		Squared
		Rooted
3067	no value	Measured	retinoic acid receptor rxr-beta. [swissprot;acc:p28702]
		Ranked
		Squared
		Rooted
3068	HECA	Measured	headcase homolog; hhdc for homolog of drosophila headcase. [refseq;acc:nm_016217]
		Ranked
		Squared
		Rooted
3069	BMP5	Measured	bone morphogenetic protein 5 precursor (bmp-5). [swissprot;acc:p22003]
		Ranked
		Squared
		Rooted
3070	MDGA1	Measured	mam domain containing glycosylphosphatidylinositol anchor 1; glycosyl-phosphatidyl-inositol-mam. [refseq;acc:nm_153487]

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.