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 1651 to 1700 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
3168	cop-coated vesicle membrane protein p24 precursor (p24a). [swissprot;acc:q15363]	TMED2	Squared
			Rooted
3169	transcriptional repressor nf-x1 (ec 6.3.2.-) (nuclear transcription factor, x box-binding, 1). [swissprot;acc:q12986]	NFX1	Measured
			Ranked
			Squared
			Rooted
3170	ecotropic virus integration 1 site protein. [swissprot;acc:q03112]	EVI1	Measured
			Ranked
			Squared
			Rooted
3171	cyclin t2. [swissprot;acc:o60583]	CCNT2	Measured
			Ranked
			Squared
			Rooted
3172	hormone sensitive lipase (ec 3.1.1.-) (hsl). [swissprot;acc:q05469]	LIPE	Measured
			Ranked
			Squared
			Rooted
3173	phosphoinositide-3-kinase, class 3; vps34; phosphatidylinositol 3-kinase, class 3. [refseq;acc:nm_002647]	PIK3C3	Measured
			Ranked
			Squared
			Rooted
3174	transmembrane 9 superfamily protein member 3 precursor (sm-11044 binding protein) (ep70-p-iso). [swissprot;acc:q9hd45]	TM9SF3	Measured
			Ranked
			Squared
			Rooted
3175	tubulin alpha-3/alpha-7 chain (alpha-tubulin 3/7). [swissprot;acc:p05214]	TUBA3D	Measured
			Ranked
			Squared
			Rooted
3176	phosphate carrier protein, mitochondrial precursor (ptp). [swissprot;acc:q00325]	SLC25A3	Measured
			Ranked
			Squared
			Rooted
3177	ergic-53 protein precursor (er-golgi intermediate compartment 53 kda protein) (lectin, mannose-binding 1) (gp58) (intracellular mannose specific lectin mr60). [swissprot;acc:p49257]	LMAN1	Measured
			Ranked
			Squared
			Rooted
3178	transcription initiation factor iie, beta subunit (tfiie-beta). [swissprot;acc:p29084]	no value	Measured
			Ranked
			Squared
			Rooted
3179	carcinoma related gene. [refseq;acc:nm_016041]	DERL2	Measured
			Ranked
			Squared
			Rooted
3180	3-hydroxyacyl-coa dehydrogenase type ii (ec 1.1.1.35) (type ii hadh) (endoplasmic reticulum-associated amyloid beta-peptide binding protein) (short-chain type dehydrogenase/reductase xh98g2). [swissprot;acc:q99714]	HSD17B10	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.