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

Results: HTML CSV LaTeX

Showing element 5808 to 5857 of 6456 in total

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

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