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

Results: HTML CSV LaTeX

Showing element 951 to 1000 of 77072 in total

green  : 0
Network Comparison Type  : Subtracted

description	Filtered	network_comparison	Value Type	Interaction Map	red	Rank
malate dehydrogenase, cytoplasmic (ec 1.1.1.37). [swissprot;acc:p40925]	1	0	Rooted	High confidence	0	3213
mam domain containing glycosylphosphatidylinositol anchor 1; glycosyl-phosphatidyl-inositol-mam. [refseq;acc:nm_153487]			Measured			3070
			Ranked
			Squared
			Rooted
membrane-bound transcription factor site 2 protease (ec 3.4.24.-) (site-2 protease) (sterol-regulatory element-binding proteins intramembrane protease). [swissprot;acc:o43462]			Measured			3215
			Ranked
			Squared
			Rooted
microfibrillar-associated protein 1. [swissprot;acc:p55081]			Measured			2949
			Ranked
			Squared
			Rooted
microtubule-interacting protein that associates with traf3; interleukin 13 receptor alpha 1-binding protein-1. [refseq;acc:nm_015650]			Measured			2880
			Ranked
			Squared
			Rooted
mitochondrial 28s ribosomal protein s30 (s30mt) (mrp-s30) (programmed cell death protein 9) (bm047). [swissprot;acc:q9np92]			Measured			3063
			Ranked
			Squared
			Rooted
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0	19.0788			19.0788	5
				Low confidence		4
		31.36	Squared	High confidence	31.36	357
				Low confidence		704
		364	Measured	High confidence	364	88
				Low confidence		170
mitochondrial 28s ribosomal protein s6 (mrp-s6). [swissprot;acc:p82932]		0		High confidence	0	496
			Squared
			Rooted
	1		Measured			2825
			Ranked
			Squared
			Rooted
mitochondrial deoxynucleotide carrier (mitochondrial uncoupling protein 1). [swissprot;acc:q9hc21]			Measured			3014
			Ranked
			Squared
			Rooted
mitochondrial ribosomal protein s7; 30s ribosomal protein s7 homolog. [refseq;acc:nm_015971]			Measured			3016
			Ranked
			Squared
			Rooted
mitochondrial solute carrier protein. [refseq;acc:nm_016612]			Measured			2915
			Ranked
			Squared
			Rooted
mitogen-activated protein kinase kinase 1 interacting protein 1 (mek binding partner 1) (mp1) (pro2783). [swissprot;acc:q9uha4]			Measured			3084
				Low confidence		5049
			Ranked	High confidence		3084
				Low confidence		5048

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
- 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.