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	red	green	network_comparison

Results: HTML CSV LaTeX

Showing element 1230 to 1279 of 2060 in total

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

Rank	Hugo	description	Value Type
3063	MRPS30	mitochondrial 28s ribosomal protein s30 (s30mt) (mrp-s30) (programmed cell death protein 9) (bm047). [swissprot;acc:q9np92]	Ranked
			Squared
			Rooted
3064	C7	complement component c7 precursor. [swissprot;acc:p10643]	Measured
			Ranked
			Squared
			Rooted
3065	WISP3	wnt1 inducible signaling pathway protein 3 isoform 1; wnt-1 signaling pathway protein 3; wnt1 signaling pathway protein 3; wnt-1 inducible signaling pathway protein 3. [refseq;acc:nm_003880]	Measured
			Ranked
			Squared
			Rooted
3066	VEGFA	vascular endothelial growth factor a precursor (vegf-a) (vascular permeability factor) (vpf). [swissprot;acc:p15692]	Measured
			Ranked
			Squared
			Rooted
3067	no value	retinoic acid receptor rxr-beta. [swissprot;acc:p28702]	Measured
			Ranked
			Squared
			Rooted
3068	HECA	headcase homolog; hhdc for homolog of drosophila headcase. [refseq;acc:nm_016217]	Measured
			Ranked
			Squared
			Rooted
3069	BMP5	bone morphogenetic protein 5 precursor (bmp-5). [swissprot;acc:p22003]	Measured
			Ranked
			Squared
			Rooted
3070	MDGA1	mam domain containing glycosylphosphatidylinositol anchor 1; glycosyl-phosphatidyl-inositol-mam. [refseq;acc:nm_153487]	Measured
			Ranked
			Squared
			Rooted
3071	STK38	serine/threonine kinase 38; serine threonine protein kinase. [refseq;acc:nm_007271]	Measured
			Ranked
			Squared
			Rooted
3072	PAK1IP1	pak1 interacting protein 1; pak1-interacting protein; pak/plc-interacting protein 1. [refseq;acc:nm_017906]	Measured
			Ranked
			Squared
			Rooted
3073	RWDD1	rwd domain containing 1; ptd013 protein; cgi-24 protein. [refseq;acc:nm_015952]	Measured
			Ranked
			Squared
			Rooted
3074	NT5DC3	tu12b1-ty protein. [refseq;acc:nm_016575]	Measured
			Ranked
			Squared
			Rooted
3075	USP5	ubiquitin carboxyl-terminal hydrolase 5 (ec 3.1.2.15) (ubiquitin thiolesterase 5) (ubiquitin-specific processing protease 5) (deubiquitinating enzyme 5) (isopeptidase t). [swissprot;acc:p45974]	Measured
			Ranked
			Squared

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.