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	Value Type	Gene	Hugo	Interaction Map	description	Filtered	network_comparison	red	green

Results: HTML CSV LaTeX

Showing element 1032 to 1081 of 2060 in total

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

Rank	Value Type	Hugo	description
3013	Rooted	CENPB	major centromere autoantigen b (centromere protein b) (cenp-b). [swissprot;acc:p07199]
3014	Measured	SLC25A19	mitochondrial deoxynucleotide carrier (mitochondrial uncoupling protein 1). [swissprot;acc:q9hc21]
	Ranked
	Squared
	Rooted
3015	Measured	NUP85	pericentrin 1; frount; nucleoporin nup75. [refseq;acc:nm_024844]
	Ranked
	Squared
	Rooted
3016	Measured	MRPS7	mitochondrial ribosomal protein s7; 30s ribosomal protein s7 homolog. [refseq;acc:nm_015971]
	Ranked
	Squared
	Rooted
3017	Measured	LRRFIP1	leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735]
	Ranked
	Squared
	Rooted
3018	Measured	CRISP1	cysteine-rich secretory protein-1 precursor (crisp-1) (acidic epididymal glycoprotein homolog) (aeg-like protein) (arp). [swissprot;acc:p54107]
	Ranked
	Squared
	Rooted
3019	Measured	KLHDC3	testis intracellular mediator protein. [refseq;acc:nm_057161]
	Ranked
	Squared
	Rooted
3020	Measured	PACSIN1	protein kinase c and casein kinase substrate in neurons protein 1. [swissprot;acc:q9by11]
	Ranked
	Squared
	Rooted
3021	Measured	CRISP2	testis-specific protein tpx-1 precursor (cysteine-rich secretory protein-2) (crisp-2). [swissprot;acc:p16562]
	Ranked
	Squared
	Rooted
3022	Measured	NAGK	n-acetylglucosamine kinase (ec 2.7.1.59) (glcnac kinase). [swissprot;acc:q9uj70]
	Ranked
	Squared
	Rooted
3023	Measured	VAPB	vesicle-associated membrane protein-associated protein b/c (vamp- associated protein b/c) (vamp-b/vamp-c) (vap-b/vap-c). [swissprot;acc:o95292]
	Ranked
	Squared
	Rooted
3024	Measured	PIGT	phosphatidylinositol glycan class t precursor. [refseq;acc:nm_015937]
	Ranked
	Squared
	Rooted
3025	Measured	HMG1L1	dj579f20.1 (high-mobility group (nonhistone chromosomal) protein 1-like 1). [sptrembl;acc:q9nqj4]
	Ranked
	Squared
	Rooted
3026	Measured	SLC36A1	solute carrier family 36 member 1; proton / amino acid symporter; lysosomal amino acid transporter 1. [refseq;acc:nm_078483]

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.