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 12214 to 12263 of 12912 in total

Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
red  : 0.00001
green  : 0.00001
network_comparison  : 1

Rank	description	Value Type
3054	double-stranded rna-binding zinc finger protein jaz. [refseq;acc:nm_012279]	Ranked
		Squared
		Rooted
3055	vacuolar atp synthase subunit h (ec 3.6.3.14) (v-atpase h subunit) (vacuolar proton pump h subunit) (v-atpase m9.2 subunit) (v-atpase 9.2 kda membrane accessory protein). [swissprot;acc:o15342]	Measured
		Ranked
		Squared
		Rooted
3056	protein transport protein sec24a (sec24-related protein a) (fragment). [swissprot;acc:o95486]	Measured
		Ranked
		Squared
		Rooted
3057	complement component c9 precursor. [swissprot;acc:p02748]	Measured
		Ranked
		Squared
		Rooted
3058	glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926]	Measured
		Ranked
		Squared
		Rooted
3059	ribonuclease iii (ec 3.1.26.3) (rnase iii) (p241). [swissprot;acc:q9nrr4]	Measured
		Ranked
		Squared
		Rooted
3060	tetratricopeptide repeat protein 1 (tpr repeat protein 1). [swissprot;acc:q99614]	Measured
		Ranked
		Squared
		Rooted
3061	kiaa1194. [refseq;acc:nm_015455]	Measured
		Ranked
		Squared
		Rooted
3062	sparc precursor (secreted protein acidic and rich in cysteine) (osteonectin) (on) (basement membrane protein bm-40). [swissprot;acc:p09486]	Measured
		Ranked
		Squared
		Rooted
3063	mitochondrial 28s ribosomal protein s30 (s30mt) (mrp-s30) (programmed cell death protein 9) (bm047). [swissprot;acc:q9np92]	Measured
		Ranked
		Squared
		Rooted
3064	complement component c7 precursor. [swissprot;acc:p10643]	Measured
		Ranked
		Squared
		Rooted
3065	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]	Measured
		Ranked
		Squared
		Rooted
3066	vascular endothelial growth factor a precursor (vegf-a) (vascular permeability factor) (vpf). [swissprot;acc:p15692]	Measured
		Ranked
		Squared

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.