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 832 to 881 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
2963	RABGGTB	Rooted	geranylgeranyl transferase type ii beta subunit (ec 2.5.1.-) (rab geranylgeranyltransferase beta subunit) (rab geranyl- geranyltransferase beta subunit) (rab gg transferase beta) (rab ggtase beta). [swissprot;acc:p53611]
2964	SEMA6D	Measured	semaphorin 6d isoform 3 precursor. [refseq;acc:nm_153617]
		Ranked
		Squared
		Rooted
2965	SLCO5A1	Measured	solute carrier family 21 member 15 (organic anion transporter polypeptide-related protein 4) (oatp-rp4) (oatprp4). [swissprot;acc:q9h2y9]
		Ranked
		Squared
		Rooted
2966	PI15	Measured	protease inhibitor 15 preproprotein; 25 kda trypsin inhibitor. [refseq;acc:nm_015886]
		Ranked
		Squared
		Rooted
2967	TAF8	Measured	taube nuss. [refseq;acc:nm_138572]
		Ranked
		Squared
		Rooted
2968	RNF144B	Measured	ba528a10.3.2 (novel protein similar to kiaa0161, isoform 2) (fragment). [sptrembl;acc:q9bx39]
		Ranked
		Squared
		Rooted
2969	TFAP2A	Measured	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]
		Ranked
		Squared
		Rooted
2970	NOV	Measured	nov protein homolog precursor (novh) (nephroblastoma overexpressed gene protein homolog). [swissprot;acc:p48745]
		Ranked
		Squared
		Rooted
2971	XPA	Measured	dna-repair protein complementing xp-a cells (xeroderma pigmentosum group a complementing protein). [swissprot;acc:p23025]
		Ranked
		Squared
		Rooted
2972	NR5A1	Measured	steroidogenic factor 1 (stf-1) (sf-1) (steroid hormone receptor ad4bp) (fushi tarazu factor homolog 1). [swissprot;acc:q13285]
		Ranked
		Squared
		Rooted
2973	ALDOB	Measured	fructose-bisphosphate aldolase b (ec 4.1.2.13) (liver-type aldolase). [swissprot;acc:p05062]
		Ranked
		Squared
		Rooted
2974	CDK9	Measured	cell division protein kinase 9 (ec 2.7.1.-) (serine/threonine-protein kinase pitalre) (c-2k). [swissprot;acc:p50750]
		Ranked
		Squared
		Rooted
2975	KCTD3	Measured	potassium channel tetramerisation domain containing 3; ny-ren-45 antigen. [refseq;acc:nm_016121]
		Ranked
		Squared
		Rooted
2976	CAB39	Measured	mo25 protein (cgi-66). [swissprot;acc:q9y376]

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.