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

Results: HTML CSV LaTeX

Showing element 851 to 900 of 2060 in total

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

Rank	description	Hugo	Value Type
2968	ba528a10.3.2 (novel protein similar to kiaa0161, isoform 2) (fragment). [sptrembl;acc:q9bx39]	RNF144B	Squared
			Rooted
2969	transcription factor ap-2 alpha (ap2-alpha) (activating enhancer- binding protein 2 alpha) (ap-2 transcription factor) (activator protein-2) (ap-2). [swissprot;acc:p05549]	TFAP2A	Measured
			Ranked
			Squared
			Rooted
2970	nov protein homolog precursor (novh) (nephroblastoma overexpressed gene protein homolog). [swissprot;acc:p48745]	NOV	Measured
			Ranked
			Squared
			Rooted
2971	dna-repair protein complementing xp-a cells (xeroderma pigmentosum group a complementing protein). [swissprot;acc:p23025]	XPA	Measured
			Ranked
			Squared
			Rooted
2972	steroidogenic factor 1 (stf-1) (sf-1) (steroid hormone receptor ad4bp) (fushi tarazu factor homolog 1). [swissprot;acc:q13285]	NR5A1	Measured
			Ranked
			Squared
			Rooted
2973	fructose-bisphosphate aldolase b (ec 4.1.2.13) (liver-type aldolase). [swissprot;acc:p05062]	ALDOB	Measured
			Ranked
			Squared
			Rooted
2974	cell division protein kinase 9 (ec 2.7.1.-) (serine/threonine-protein kinase pitalre) (c-2k). [swissprot;acc:p50750]	CDK9	Measured
			Ranked
			Squared
			Rooted
2975	potassium channel tetramerisation domain containing 3; ny-ren-45 antigen. [refseq;acc:nm_016121]	KCTD3	Measured
			Ranked
			Squared
			Rooted
2976	mo25 protein (cgi-66). [swissprot;acc:q9y376]	CAB39	Measured
			Ranked
			Squared
			Rooted
2977	cytochrome p450 27, mitochondrial precursor (ec 1.14.-.-) (cytochrome p-450c27/25) (sterol 26-hydroxylase) (sterol 27-hydroxylase) (vitamin d(3) 25-hydroxylase) (5-beta-cholestane-3-alpha,7-alpha,12-alpha-triol 27-hydroxylase). [swissprot;acc:q02318]	CYP27A1	Measured
			Ranked
			Squared
			Rooted
2978	integrin alpha-7 precursor. [swissprot;acc:q13683]	ITGA7	Measured
			Ranked
			Squared
			Rooted
2979	udp-glucuronosyltransferase 2b28 precursor, microsomal (ec 2.4.1.17). [swissprot;acc:q9by64]	UGT2B28	Measured
			Ranked
			Squared
			Rooted
2980	ste20-like kinase; ste2-like kinase. [refseq;acc:nm_016281]	TAOK3	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.