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

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Showing element 451 to 500 of 14920 in total

Network Comparison Type  : Divided
Interaction Map  : High confidence

description	Rank	Value Type	green	Filtered	red	network_comparison
5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646]	751	Rooted	71.4638	1	66.9738	1.06704
	875	Ranked	203.954		212.002	1.03946
5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619]	596	Squared	40434.5		34129.6	1.18473
	686	Measured	7747.63		6920.69	1.11949
	749	Rooted	71.4637		66.9737	1.06704
	874	Ranked	203.954		212.002	1.03946
5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0]	601	Squared	40434.5		34129.6	1.18473
	692	Measured	7747.63		6920.69	1.11949
	756	Rooted	71.4637		66.9737	1.06704
	880	Ranked	203.954		212.002	1.03946
5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9]	599	Squared	40434.5		34129.6	1.18473
	690	Measured	7747.63		6920.69	1.11949
	754	Rooted	71.4637		66.9737	1.06704
	878	Ranked	203.954		212.002	1.03946
5'-methylthioadenosine phosphorylase (ec 2.4.2.28) (mta phosphorylase) (mtapase). [swissprot;acc:q13126]	1192	Squared	24612.9		21639	1.13743
	1606	Measured	5606.53		5232.99	1.07138
	1769	Ranked	225.734		223.016	1.01219
	2302	Rooted	60.5463		59.4004	1.01929
5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643]	57	Measured	142.417	0	270.264	1.89769
	65	Squared	15.1833		50.642	3.33538
	83	Rooted	8.12243		10.9038	1.34243
	288	Ranked	16053		14930.6	1.07517
	981	Rooted	65.3733	1	61.9129	1.05589
	1021	Ranked	214.409		221.278	1.03204
	1229	Measured	6509.74		5998.69	1.08519
	2161	Squared	32683.2		30116.4	1.08523
5-aminolevulinic acid synthase, erythroid-specific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-e). [swissprot;acc:p22557]	786		31927.7		27407.7	1.16492
	1910	Measured	7287.27		6858.84	1.06246
	2312	Rooted	71.8706		70.5239	1.0191
	2491	Ranked	195.08		194.527	1.00284
5-aminolevulinic acid synthase, nonspecific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-h). [swissprot;acc:p13196]	287	Measured	808.929	0	726.245	1.11385
	335	Rooted	25.588		24.2756	1.05406
	412	Ranked	8279.69		8546.06	1.03217
	419	Squared	212.386		202.436	1.04915
	791		31927.7	1	27407.7	1.16492
	1915	Measured	7287.27		6858.84	1.06246
	2317	Rooted	71.8706		70.5239	1.0191
	2496	Ranked	195.08		194.527	1.00284
5-formyltetrahydrofolate cyclo-ligase (ec 6.3.3.2) (5,10-methenyl- tetrahydrofolate synthetase) (methenyl-thf synthetase) (mthfs). [swissprot;acc:p49914]	1635	Squared	30221.1		27290.4	1.10739
	1833	Measured	6572.85		6175.23	1.06439
	2095	Rooted	66.4806		64.8399	1.0253
	2754	Ranked	210.642		210.638	1.00002
5-methyltetrahydrofolate--homocysteine methyltransferase (ec 2.1.1.13) (methionine synthase, vitamin-b12 dependent) (ms). [swissprot;acc:q99707]	941	Squared	30020.3		26005.2	1.1544
	1115	Measured	6314.19		5795.13	1.08957
	1362	Rooted	64.0358		61.5231	1.04084
	1921	Ranked	219.386		221.607	1.01012
54 kda nuclear rna- and dna-binding protein (p54(nrb)) (p54nrb) (55 kda nuclear protein) (nmt55) (non-pou domain-containing octamer- binding protein) (dna-binding p52/p100 complex, 52 kda subunit). [swissprot;acc:q15233]	353	Squared	57399.3		71383	1.24362
	2028	Measured	9686.82		10243.4	1.05746
	2532	Ranked	190.812		190.405	1.00214
	2636	Rooted	79.843		80.3593	1.00647

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.