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 208 to 257 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
2807	RAB1C	Rooted	ras-related protein rab-1b. [swissprot;acc:q9h0u4]
2808	LIG4	Measured	dna ligase iv (ec 6.5.1.1) (polydeoxyribonucleotide synthase [atp]). [swissprot;acc:p49917]
		Ranked
		Squared
		Rooted
2809	PHC3	Measured	polyhomeotic like 3; early development regulator 3; polyhomeotic 3. [refseq;acc:nm_024947]
		Ranked
		Squared
		Rooted
2810	UGT2A1	Measured	udp glycosyltransferase 2 family, polypeptide a1; udp glucuronosyltransferase 2 family, polypeptide a1. [refseq;acc:nm_006798]
		Ranked
		Squared
		Rooted
2811	VEGFB	Measured	vascular endothelial growth factor b precursor (vegf-b) (vegf related factor) (vrf). [swissprot;acc:p49765]
		Ranked
		Squared
		Rooted
2812	MOBKL2A	Measured	mob-lak. [refseq;acc:nm_130807]
		Ranked
		Squared
		Rooted
2813	HDAC3	Measured	histone deacetylase 3 (hd3) (rpd3-2). [swissprot;acc:o15379]
		Ranked
		Squared
		Rooted
2814	SPSB1	Measured	spry domain-containing socs box protein ssb-1. [refseq;acc:nm_025106]
		Ranked
		Squared
		Rooted
2815	NMUR1	Measured	g protein-coupled receptor 66. [refseq;acc:nm_006056]
		Ranked
		Squared
		Rooted
2816	TIGD1	Measured	tigger transposable element derived 1; jerky (mouse) homolog-like. [refseq;acc:nm_145702]
		Ranked
		Squared
		Rooted
2817	TBCA	Measured	tubulin-specific chaperone a (tubulin-folding cofactor a) (cfa) (tcp1-chaperonin cofactor a). [swissprot;acc:o75347]
		Ranked
		Squared
		Rooted
2818	UGT2B7	Measured	udp-glucuronosyltransferase 2b7 precursor, microsomal (ec 2.4.1.17) (udpgt) (3,4-catechol estrogen specific) (udpgth-2). [swissprot;acc:p16662]
		Ranked
		Squared
		Rooted
2819	no value	Measured	udp-glucuronosyltransferase 2b11 precursor, microsomal (ec 2.4.1.17) (udpgt). [swissprot;acc:o75310]
		Ranked
		Squared
		Rooted
2820		Measured	peregrin (bromodomain and phd finger-containing protein 1) (br140 protein). [swissprot;acc:p55201]

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.