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 1012 to 1061 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
3008	NUP214	Rooted	nuclear pore complex protein nup214 (nucleoporin nup214) (214 kda nucleoporin) (can protein). [swissprot;acc:p35658]
3009	COX6B1	Measured	cytochrome c oxidase polypeptide vib (ec 1.9.3.1) (aed). [swissprot;acc:p14854]
		Ranked
		Squared
		Rooted
3010	UROD	Measured	uroporphyrinogen decarboxylase (ec 4.1.1.37) (uro-d) (upd). [swissprot;acc:p06132]
		Ranked
		Squared
		Rooted
3011	MCM8	Measured	dna replication licensing factor mcm8 (minichromosome maintenance 8). [swissprot;acc:q9uja3]
		Ranked
		Squared
		Rooted
3012	SNRPB	Measured	small nuclear ribonucleoprotein associated proteins b and b' (snrnp-b) (sm protein b/b') (sm-b/sm-b') (smb/smb'). [swissprot;acc:p14678]
		Ranked
		Squared
		Rooted
3013	CENPB	Measured	major centromere autoantigen b (centromere protein b) (cenp-b). [swissprot;acc:p07199]
		Ranked
		Squared
		Rooted
3014	SLC25A19	Measured	mitochondrial deoxynucleotide carrier (mitochondrial uncoupling protein 1). [swissprot;acc:q9hc21]
		Ranked
		Squared
		Rooted
3015	NUP85	Measured	pericentrin 1; frount; nucleoporin nup75. [refseq;acc:nm_024844]
		Ranked
		Squared
		Rooted
3016	MRPS7	Measured	mitochondrial ribosomal protein s7; 30s ribosomal protein s7 homolog. [refseq;acc:nm_015971]
		Ranked
		Squared
		Rooted
3017	LRRFIP1	Measured	leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735]
		Ranked
		Squared
		Rooted
3018	CRISP1	Measured	cysteine-rich secretory protein-1 precursor (crisp-1) (acidic epididymal glycoprotein homolog) (aeg-like protein) (arp). [swissprot;acc:p54107]
		Ranked
		Squared
		Rooted
3019	KLHDC3	Measured	testis intracellular mediator protein. [refseq;acc:nm_057161]
		Ranked
		Squared
		Rooted
3020	PACSIN1	Measured	protein kinase c and casein kinase substrate in neurons protein 1. [swissprot;acc:q9by11]
		Ranked
		Squared
		Rooted
3021	CRISP2	Measured	testis-specific protein tpx-1 precursor (cysteine-rich secretory protein-2) (crisp-2). [swissprot;acc:p16562]

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.