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

Results: HTML CSV LaTeX

Showing element 11764 to 11813 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
2941	transcription initiation factor tfiid 105 kda subunit (tafii-105) (tafii105) (fragment). [swissprot;acc:q92750]	Rooted
2942	ssxt protein (synovial sarcoma, translocated to x chromosome) (syt protein). [swissprot;acc:q15532]	Measured
		Ranked
		Squared
		Rooted
2943	phosphoribosyl pyrophosphate synthetase-associated protein 2 (prpp synthetase-associated protein 2) (41 kda phosphoribosypyrophosphate synthetase-associated protein) (pap41). [swissprot;acc:o60256]	Measured
		Ranked
		Squared
		Rooted
2944	tigger transposable element derived 7; jerky (mouse) homolog-like. [refseq;acc:nm_033208]	Measured
		Ranked
		Squared
		Rooted
2945	tropomyosin 1 alpha chain (alpha-tropomyosin). [swissprot;acc:p09493]	Measured
		Ranked
		Squared
		Rooted
2946	transcription initiation factor iia gamma chain (tfiia p12 subunit) (tfiia-12) (tfiias) (tfiia-gamma). [swissprot;acc:p52657]	Measured
		Ranked
		Squared
		Rooted
2947	small edrk-rich factor 2. [refseq;acc:nm_005770]	Measured
		Ranked
		Squared
		Rooted
2948	transcription factor 12 (transcription factor htf-4) (e-box-binding protein) (dna-binding protein htf4). [swissprot;acc:q99081]	Measured
		Ranked
		Squared
		Rooted
2949	microfibrillar-associated protein 1. [swissprot;acc:p55081]	Measured
		Ranked
		Squared
		Rooted
2950	bax inhibitor-1 (bi-1) (testis enhanced gene transcript). [swissprot;acc:p55061]	Measured
		Ranked
		Squared
		Rooted
2951	integrin beta-7 precursor. [swissprot;acc:p26010]	Measured
		Ranked
		Squared
		Rooted
2952	serine/threonine-protein kinase receptor r3 precursor (ec 2.7.1.37) (skr3) (activin receptor-like kinase 1) (alk-1) (tgf-b superfamily receptor type i) (tsr-i). [swissprot;acc:p37023]	Measured
		Ranked
		Squared
		Rooted
2953	glioma pathogenesis-related protein (glipr) (rtvp-1 protein). [swissprot;acc:p48060]	Measured
		Ranked
		Squared
		Rooted
2954	nadh-ubiquinone oxidoreductase 39 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-39kd) (ci-39kd). [swissprot;acc:q16795]	Measured

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.