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.

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

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

Results: HTML CSV LaTeX

Showing element 6358 to 6407 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

Rank	Network Comparison Type	Value Type	description	network_comparison	red	green
795	Subtracted	Ranked	palmitoyl-protein thioesterase 1 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 1). [swissprot;acc:p50897]	9.399	212.386	221.785
		Squared	branched-chain amino acid aminotransferase, cytosolic (ec 2.6.1.42) (bcat(c)) (eca39 protein). [swissprot;acc:p54687]	3986.5	23958.6	27945.1
		Rooted	tbc1 domain family member 5. [swissprot;acc:q92609]	4.0968	65.0565	69.1533
796	Divided	Measured	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	1.11061	6834.54	7590.49
		Ranked	placental thrombin inhibitor (cytoplasmic antiproteinase) (cap) (protease inhibitor 6) (pi-6). [swissprot;acc:p35237]	1.04578	224.244	234.511
		Squared	xpmc2 prevents mitotic catastrophe 2 homolog; xenopus prevents mitotic catastrophe 2 homolog. [refseq;acc:nm_020385]	1.16451	25842.1	30093.4
		Rooted	set domain and mariner transposase fusion gene. [refseq;acc:nm_006515]	1.06481	54.765	51.4319
	Subtracted	Measured	integral membrane protein 2b (transmembrane protein bri) [contains: abri/adan amyloid peptide]. [swissprot;acc:q9y287]	613.46	6362.64	6976.1
		Ranked	beta-soluble nsf attachment protein (snap-beta) (n-ethylmaleimide- sensitive factor attachment protein, beta). [swissprot;acc:q9h115]	9.399	212.386	221.785
		Squared	branched-chain amino acid aminotransferase, mitochondrial precursor (ec 2.6.1.42) (bcat(m)) (placental protein 18) (pp18). [swissprot;acc:o15382]	3985.8	23966.4	27952.2
		Rooted	tubby related protein 1 (tubby-like protein 1). [swissprot;acc:o00294]	4.0968	65.0565	69.1533
797	Divided	Measured	importin beta-1 subunit (karyopherin beta-1 subunit) (nuclear factor p97) (importin 90). [swissprot;acc:q14974]	1.11061	6834.54	7590.49
		Ranked	cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452]	1.04578	224.244	234.511
		Squared	limbic system-associated membrane protein precursor (lsamp). [swissprot;acc:q13449]	1.16433	22535.2	26238.4
		Rooted	structure-specific recognition protein 1 (ssrp1) (recombination signal sequence recognition protein) (t160) (chromatin-specific transcription elongation factor 80 kda subunit) (fact 80 kda subunit). [swissprot;acc:q08945]	1.06481	54.1622	57.6725
	Subtracted	Measured	integral membrane protein 2c (transmembrane protein bri3) (npd018). [swissprot;acc:q9nqx7]	613.46	6362.64	6976.1
		Ranked	syntaxin 16 (syn16). [swissprot;acc:o14662]	9.399	212.386	221.785
		Squared	transcription factor p65 (nuclear factor nf-kappa-b p65 subunit). [swissprot;acc:q04206]	3985	46338.5	42353.5
		Rooted	vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [swissprot;acc:q9ubq0]	4.0968	65.0565	69.1533
798	Divided	Measured	transducin beta-like 1x protein (transducin-beta-like 1, x-linked). [swissprot;acc:o60907]	1.11061	6834.54	7590.49
		Ranked	leukocyte elastase inhibitor (lei) (monocyte/neutrophil elastase inhibitor) (m/nei) (ei). [swissprot;acc:p30740]	1.04578	224.244	234.511
		Squared	opioid binding protein/cell adhesion molecule precursor (obcam) (opioid-binding cell adhesion molecule) (opcml). [swissprot;acc:q14982]	1.1642	22587.2	26296.1
		Rooted	cd209 antigen-like; putative type ii membrane protein. [refseq;acc:nm_014257]	1.06481	54.765	51.4319
	Subtracted	Measured	integral membrane protein 2a (e25 protein). [swissprot;acc:o43736]	613.46	6362.64	6976.1
		Ranked	27 kda golgi snare protein (golgi snap receptor complex member 2) (membrin). [swissprot;acc:o14653]	9.399	212.386	221.785
		Squared	transcription factor relb (i-rel). [swissprot;acc:q01201]	3985	46338.5	42353.5
		Rooted	numb-like protein (numb-r). [swissprot;acc:q9y6r0]	4.0968	65.0565	69.1533
799	Divided	Measured	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	1.11061	6834.54	7590.49
		Ranked	sequestosome 1; ubiquitin-binding protein p62; phosphotyrosine independent ligand for the lck sh2 domain p62. [refseq;acc:nm_003900]	1.04501	221.965	212.404
		Squared	neurotrimin precursor (hnt). [swissprot;acc:q9p121]	1.16412	22623.7	26336.8
		Rooted	low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734]	1.06481	54.765	51.4319
	Subtracted	Measured	dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882]	611.86	5222.71	5834.57
		Ranked	syntaxin 1a (neuron-specific antigen hpc-1). [swissprot;acc:q16623]	9.399	212.386	221.785
		Squared	nf-kappab inhibitor alpha (major histocompatibility complex enhancer- binding protein mad3) (i-kappa-b-alpha) (ikappabalpha) (ikb-alpha). [swissprot;acc:p25963]	3985	46338.5	42353.5
		Rooted	tubby related protein 3 (tubby-like protein 3). [swissprot;acc:o75386]	4.0968	65.0565	69.1533
800	Divided	Measured	orphan nuclear receptor nr6a1 (germ cell nuclear factor) (gcnf) (retinoid receptor-related testis specific receptor) (rtr). [swissprot;acc:q15406]	1.1105	6075.55	6746.92
		Ranked	nonspecific lipid-transfer protein, mitochondrial precursor (nsl-tp) (sterol carrier protein 2) (scp-2) (sterol carrier protein x) (scp-x) (scpx). [swissprot;acc:p22307]	1.04501	221.965	212.404
		Squared	phosphomannomutase 2 (ec 5.4.2.8) (pmm 2). [swissprot;acc:o15305]	1.1634	22210.6	25839.9
		Rooted	chromatin-specific transcription elongation factor large subunit. [refseq;acc:nm_007192]	1.06481	54.1622	57.6725
	Subtracted	Measured	ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701]	611.39	3583.56	4194.95
		Ranked	alpha-soluble nsf attachment protein (snap-alpha) (n-ethylmaleimide- sensitive factor attachment protein, alpha). [swissprot;acc:p54920]	9.399	212.386	221.785
		Squared	coproporphyrinogen iii oxidase, mitochondrial precursor (ec 1.3.3.3) (coproporphyrinogenase) (coprogen oxidase) (cox). [swissprot;acc:p36551]	3985	46338.5	42353.5
		Rooted	vacuolar protein sorting 35 (vesicle protein sorting 35) (hvps35) (maternal-embryonic 3). [swissprot;acc:q96qk1]	4.0968	65.0565	69.1533
801	Divided	Measured	importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [swissprot;acc:o00505]	1.1105	6456.35	7169.75
		Ranked	beta-catenin (pro2286). [swissprot;acc:p35222]	1.04445	224.445	214.894
		Squared	phosphomannomutase 1 (ec 5.4.2.8) (pmm 1) (pmmh-22). [swissprot;acc:q92871]	1.16322	22208.7	25833.6
		Rooted	cd209 antigen; dendritic cell-specific icam3-grabbing nonintegrin. [refseq;acc:nm_021155]	1.06481	54.765	51.4319
	Subtracted	Measured	neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784]	611.163	779.167	1390.33
		Ranked	adipocyte plasma membrane-associated protein (bscv protein). [swissprot;acc:q9hdc9]	9.399	212.386	221.785
		Squared	werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [refseq;acc:nm_020135]	3982.8	20613.1	24595.9

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.