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	green	Filtered	red	network_comparison

Results: HTML CSV LaTeX

Showing element 5858 to 5907 of 6456 in total

Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Network Comparison Type	green	red	network_comparison
2929	lysosomal trafficking regulator (beige homolog). [swissprot;acc:q99698]	Subtracted	0	0	0
2930	interleukin enhancer binding factor 2; nuclear factor of activated t-cells, 45-kda. [refseq;acc:nm_004515]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2931	tropomyosin alpha 3 chain (tropomyosin 3) (tropomyosin gamma). [swissprot;acc:p06753]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2932	pogo transposable element with znf domain isoform 1. [refseq;acc:nm_015100]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2933	semaphorin 6c precursor (semaphorin y) (sema y). [swissprot;acc:q9h3t2]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2934	protoporphyrinogen oxidase (ec 1.3.3.4) (ppo). [swissprot;acc:p50336]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2935	putative membrane protein. [refseq;acc:nm_019026]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2936	retinoic acid receptor rxr-gamma. [swissprot;acc:p48443]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2937	similar to mob-lak. [refseq;acc:nm_145279]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2938	cyr61 protein precursor (cysteine-rich, angiogenic inducer, 61) (insulin-like growth factor-binding protein 10) (gig1 protein). [swissprot;acc:o00622]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2939	fibrillin 3. [refseq;acc:nm_032447]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2940	transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [swissprot;acc:p15884]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2941	transcription initiation factor tfiid 105 kda subunit (tafii-105) (tafii105) (fragment). [swissprot;acc:q92750]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2942	ssxt protein (synovial sarcoma, translocated to x chromosome) (syt protein). [swissprot;acc:q15532]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2943	phosphoribosyl pyrophosphate synthetase-associated protein 2 (prpp synthetase-associated protein 2) (41 kda phosphoribosypyrophosphate synthetase-associated protein) (pap41). [swissprot;acc:o60256]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2944	tigger transposable element derived 7; jerky (mouse) homolog-like. [refseq;acc:nm_033208]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2945	tropomyosin 1 alpha chain (alpha-tropomyosin). [swissprot;acc:p09493]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2946	transcription initiation factor iia gamma chain (tfiia p12 subunit) (tfiia-12) (tfiias) (tfiia-gamma). [swissprot;acc:p52657]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2947	small edrk-rich factor 2. [refseq;acc:nm_005770]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2948	transcription factor 12 (transcription factor htf-4) (e-box-binding protein) (dna-binding protein htf4). [swissprot;acc:q99081]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2949	microfibrillar-associated protein 1. [swissprot;acc:p55081]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2950	bax inhibitor-1 (bi-1) (testis enhanced gene transcript). [swissprot;acc:p55061]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2951	integrin beta-7 precursor. [swissprot;acc:p26010]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
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]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2953	glioma pathogenesis-related protein (glipr) (rtvp-1 protein). [swissprot;acc:p48060]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
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]	Divided	0.00001	0.00001	1

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.