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

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Showing element 3682 to 3731 of 77072 in total

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Value Type  : Ranked

green	network_comparison	Rank	Interaction Map	description	red	Network Comparison Type
10641.7	1662	147	High confidence	tubby protein homolog. [swissprot;acc:p50607]	12303.7	Subtracted
10644.4	1.03142	414		germ cell-less. [refseq;acc:nm_022471]	10978.8	Divided
	334.4	409				Subtracted
10646.1	1.00406	808	Low confidence	intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3]	10603	Divided
	43.1	806				Subtracted
10653.8	1.0145	729		40s ribosomal protein s29. [swissprot;acc:p30054]	10808.3	Divided
	154.5	733				Subtracted
10665.1	1.03816	383	High confidence	chromodomain y-like protein 2. [refseq;acc:nm_152342]	10273.1	Divided
	392	388				Subtracted
10665.3	1.01501	726	Low confidence	sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [swissprot;acc:p50993]	10507.6	Divided
	157.7	728				Subtracted
10670.2	1.08309	392		alpha-amylase, salivary precursor (ec 3.2.1.1) (1,4-alpha-d-glucan glucanohydrolase). [swissprot;acc:p04745]	9851.59	Divided
	818.61	331				Subtracted
10671.1	1.0506	535		cytochrome c oxidase subunit viia-l related protein, mitochondrial precursor. [swissprot;acc:o60397]	11211.1	Divided
	540	550				Subtracted
10680.5	1.15176	162	High confidence	putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642]	12301.4	Divided
	1620.9	152				Subtracted
10686.7	1.03727	385		testis-specific chromodomain protein y protein 2. [swissprot;acc:q9y6f7]	10302.7	Divided
	384	391				Subtracted
10687.4	1.03724	386		testis-specific chromodomain y protein 1. [swissprot;acc:q9y6f8]	10303.7	Divided
	383.7	392				Subtracted
10695.6	1.03993	376		ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930]	10284.9	Divided
	410.7	381				Subtracted
10700.6	1.007	788	Low confidence	galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470]	10775.5	Divided
	74.9	789				Subtracted
10702.3	1.06521	470		glutamate dehydrogenase 2, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p49448]	11400.2	Divided
	697.9	376				Subtracted
10710.2	1.04974	538		cytochrome c oxidase polypeptide viia-heart, mitochondrial precursor (ec 1.9.3.1) (cytochrome c oxidase subunit viia-h) (cox viia-m). [swissprot;acc:p24310]	11242.9	Divided
	532.7	552				Subtracted
10716	1.05681	511		zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623]	11324.8	Divided
	608.8	405				Subtracted
10723.7	1.13203	179	High confidence	mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426]	9473.01	Divided
	1250.69	191				Subtracted
10736.4	1.03044	620	Low confidence	tolloid-like 1. [refseq;acc:nm_012464]	10419.2	Divided
	317.2	623				Subtracted
10741	1.03902	596		phospholipase b. [refseq;acc:nm_153021]	10337.6	Divided
	403.4	597				Subtracted
10757.5	1.03453	607		60s ribosomal protein l17 (l23). [swissprot;acc:p18621]	11129	Divided
	371.5	605				Subtracted
10763.4	1.08181	278	High confidence	associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799]	11644	Divided
	880.6	270				Subtracted
10763.7	1.09124	367	Low confidence	60s ribosomal protein l23a. [swissprot;acc:p29316]	11745.8	Divided
	982.1	269				Subtracted
10764.4	1.09148	365		c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02]	11749.1	Divided
	984.7	266				Subtracted
10771	1.48976	38	High confidence	cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336]	7230	Divided
	3541	53				Subtracted
10772	1.01041	758	Low confidence	dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9]	10661	Divided
	111	756				Subtracted
10779.4	1.0766	428		60s ribosomal protein l21. [swissprot;acc:p46778]	11605.1	Divided

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.