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	Network Comparison Type	Value Type	Interaction Map	red	network_comparison	Filtered	green

Results: HTML CSV LaTeX

Showing element 5808 to 5857 of 6456 in total

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

Rank	description	Network Comparison Type	red	network_comparison	green
2904	6-pyruvoyl tetrahydrobiopterin synthase (ec 4.2.3.12) (ptps) (ptp synthase). [swissprot;acc:q03393]	Subtracted	0	0	0
2905	integrin beta-1 precursor (fibronectin receptor beta subunit) (cd29 antigen) (integrin vla-4 beta subunit). [swissprot;acc:p05556]	Divided	0.00001	1	0.00001
		Subtracted	0	0	0
2906	thousand and one amino acid protein kinase. [refseq;acc:nm_004783]	Divided	0.00001	1	0.00001
		Subtracted	0	0	0
2907	fructose-bisphosphate aldolase a (ec 4.1.2.13) (muscle-type aldolase) (lung cancer antigen ny-lu-1). [swissprot;acc:p04075]	Divided	0.00001	1	0.00001
		Subtracted	0	0	0
2908	serine/threonine-protein kinase chk1 (ec 2.7.1.-). [swissprot;acc:o14757]	Divided	0.00001	1	0.00001
		Subtracted	0	0	0
2909	nk6 transcription factor related, locus 2; nk homeobox family 6, b; glial and testis-specific homeobox protein; homeobox 6b. [refseq;acc:nm_177400]	Divided	0.00001	1	0.00001
		Subtracted	0	0	0
2910	protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992]	Divided	0.00001	1	0.00001
		Subtracted	0	0	0
2911	bup protein. [refseq;acc:nm_012071]	Divided	0.00001	1	0.00001
		Subtracted	0	0	0
2912	inositol polyphosphate-5-phosphatase; phosphatidylinositol polyphosphate 5-phosphatase type iv; phosphatidylinositol (4,5) bisphosphate 5-phosphatase. [refseq;acc:nm_019892]	Divided	0.00001	1	0.00001
		Subtracted	0	0	0
2913	au rna-binding protein/enoyl-coenzyme a hydratase precursor; au rna-binding protein/enoyl-coenzyme a hydratase; 3-methylglutaconyl-coa hydratase; mga type i. [refseq;acc:nm_001698]	Divided	0.00001	1	0.00001
		Subtracted	0	0	0
2914	lactamase, beta 2. [refseq;acc:nm_016027]	Divided	0.00001	1	0.00001
		Subtracted	0	0	0
2915	mitochondrial solute carrier protein. [refseq;acc:nm_016612]	Divided	0.00001	1	0.00001
		Subtracted	0	0	0
2916	ribose-phosphate pyrophosphokinase i (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase i) (ppribp) (prs-i). [swissprot;acc:p09329]	Divided	0.00001	1	0.00001
		Subtracted	0	0	0
2917	t-complex protein 1, zeta subunit (tcp-1-zeta) (cct-zeta) (cct-zeta-1) (tcp20) (htr3). [swissprot;acc:p40227]	Divided	0.00001	1	0.00001
		Subtracted	0	0	0
2918	nipsnap2 protein (glioblastoma amplified sequence). [swissprot;acc:o75323]	Divided	0.00001	1	0.00001
		Subtracted	0	0	0
2919	glycine receptor alpha-1 chain precursor (glycine receptor 48 kda subunit) (strychnine binding subunit). [swissprot;acc:p23415]	Divided	0.00001	1	0.00001
		Subtracted	0	0	0
2920	glycine receptor alpha-3 chain precursor. [swissprot;acc:o75311]	Divided	0.00001	1	0.00001
		Subtracted	0	0	0
2921	ell-associated factor 2; uncharacterized bone marrow protein bm040; testosterone regulated apoptosis inducer and tumor suppressor. [refseq;acc:nm_018456]	Divided	0.00001	1	0.00001
		Subtracted	0	0	0
2922	10-formyltetrahydrofolate dehydrogenase (ec 1.5.1.6) (10-fthfdh). [swissprot;acc:o75891]	Divided	0.00001	1	0.00001
		Subtracted	0	0	0
2923	transmembrane protein 4. [refseq;acc:nm_014255]	Divided	0.00001	1	0.00001
		Subtracted	0	0	0
2924	rcd1 required for cell differentiation1 homolog; protein involved in sexual development; rcd1 (required for cell differentiation, s.pombe) homolog 1. [refseq;acc:nm_005444]	Divided	0.00001	1	0.00001
		Subtracted	0	0	0
2925	ras-related protein ral-b. [swissprot;acc:p11234]	Divided	0.00001	1	0.00001
		Subtracted	0	0	0
2926	dual specificity protein phosphatase 11 (ec 3.1.3.48) (rna/rnp complex-intereracting phosphatase) (phosphatase that interacts with rna/rnp complex 1). [swissprot;acc:o75319]	Divided	0.00001	1	0.00001
		Subtracted	0	0	0
2927	wd-repeat containing protein ciao 1. [swissprot;acc:o76071]	Divided	0.00001	1	0.00001
		Subtracted	0	0	0
2928	calmodulin. [swissprot;acc:p02593]	Divided	0.00001	1	0.00001
		Subtracted	0	0	0
2929	lysosomal trafficking regulator (beige homolog). [swissprot;acc:q99698]	Divided	0.00001	1	0.00001

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.