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

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Showing element 11714 to 11763 of 12912 in total

Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
red  : 0.00001
green  : 0.00001
network_comparison  : 1

Rank	description	Value Type
2929	lysosomal trafficking regulator (beige homolog). [swissprot;acc:q99698]	Ranked
		Squared
		Rooted
2930	interleukin enhancer binding factor 2; nuclear factor of activated t-cells, 45-kda. [refseq;acc:nm_004515]	Measured
		Ranked
		Squared
		Rooted
2931	tropomyosin alpha 3 chain (tropomyosin 3) (tropomyosin gamma). [swissprot;acc:p06753]	Measured
		Ranked
		Squared
		Rooted
2932	pogo transposable element with znf domain isoform 1. [refseq;acc:nm_015100]	Measured
		Ranked
		Squared
		Rooted
2933	semaphorin 6c precursor (semaphorin y) (sema y). [swissprot;acc:q9h3t2]	Measured
		Ranked
		Squared
		Rooted
2934	protoporphyrinogen oxidase (ec 1.3.3.4) (ppo). [swissprot;acc:p50336]	Measured
		Ranked
		Squared
		Rooted
2935	putative membrane protein. [refseq;acc:nm_019026]	Measured
		Ranked
		Squared
		Rooted
2936	retinoic acid receptor rxr-gamma. [swissprot;acc:p48443]	Measured
		Ranked
		Squared
		Rooted
2937	similar to mob-lak. [refseq;acc:nm_145279]	Measured
		Ranked
		Squared
		Rooted
2938	cyr61 protein precursor (cysteine-rich, angiogenic inducer, 61) (insulin-like growth factor-binding protein 10) (gig1 protein). [swissprot;acc:o00622]	Measured
		Ranked
		Squared
		Rooted
2939	fibrillin 3. [refseq;acc:nm_032447]	Measured
		Ranked
		Squared
		Rooted
2940	transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [swissprot;acc:p15884]	Measured
		Ranked
		Squared
		Rooted
2941	transcription initiation factor tfiid 105 kda subunit (tafii-105) (tafii105) (fragment). [swissprot;acc:q92750]	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
- 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.