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	description	Value Type	Interaction Map	Filtered	network_comparison	red	green

Results: HTML CSV LaTeX

Showing element 1175 to 1224 of 1892 in total

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

Rank	Hugo	description	Value Type
3049	SLC30A3	zinc transporter 3 (znt-3). [swissprot;acc:q99726]	Squared
			Rooted
3050	ACVR1	activin receptor type i precursor (ec 2.7.1.37) (actr-i) (serine/threonine-protein kinase receptor r1) (skr1) (activin receptor-like kinase 2) (alk-2) (tgf-b superfamily receptor type i) (tsr-i). [swissprot;acc:q04771]	Measured
			Ranked
			Squared
			Rooted
3051	CYB561D2	putative tumor suppressor 101f6. [refseq;acc:nm_007022]	Measured
			Ranked
			Squared
			Rooted
3052	PDCD10	programmed cell death 10; apoptosis-related protein 15. [refseq;acc:nm_007217]	Measured
			Ranked
			Squared
			Rooted
3053	HGD	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]	Measured
			Ranked
			Squared
			Rooted
3054	ZNF346	double-stranded rna-binding zinc finger protein jaz. [refseq;acc:nm_012279]	Measured
			Ranked
			Squared
			Rooted
3055	ATP6V0E1	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	SEC24A	protein transport protein sec24a (sec24-related protein a) (fragment). [swissprot;acc:o95486]	Measured
			Ranked
			Squared
			Rooted
3057	C9	complement component c9 precursor. [swissprot;acc:p02748]	Measured
			Ranked
			Squared
			Rooted
3058	GNPDA1	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	RNASEN	ribonuclease iii (ec 3.1.26.3) (rnase iii) (p241). [swissprot;acc:q9nrr4]	Measured
			Ranked
			Squared
			Rooted
3060	TTC1	tetratricopeptide repeat protein 1 (tpr repeat protein 1). [swissprot;acc:q99614]	Measured
			Ranked
			Squared
			Rooted
3061	CNOT6	kiaa1194. [refseq;acc:nm_015455]	Measured
			Ranked
			Squared
			Rooted

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.