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

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Showing element 601 to 650 of 38536 in total

Filtered  : 0
Network Comparison Type  : Divided

description	Value Type	Rank	network_comparison	Interaction Map	green	red
arp2/3 complex 41 kda subunit (p41-arc) (actin-related protein 2/3 complex subunit 1b). [swissprot;acc:o15143]	Measured	337	1.07624	High confidence	2194.52	2039.07
		573	1.04544	Low confidence	1802.55	1884.45
	Ranked	360	1.0936		11628.7	10633.4
		449	1.02129	High confidence	9690.83	9897.12
	Squared	321	1.162		6590.82	5671.94
		650	1.05148	Low confidence	9625.85	10121.4
	Rooted	364	1.09791		24.2926	26.6711
		464	1.01265	High confidence	30.7252	30.3413
arsenical pump-driving atpase (ec 3.6.3.16) (arsenite-translocating atpase) (arsenical resistance atpase) (arsenite-transporting atpase) (arsa) (asna-i). [swissprot;acc:o43681]	Measured	213	1.18471		1376.88	1162.21
		582	1.04225	Low confidence	1319.88	1266.38
	Ranked	264	1.08947	High confidence	10935.1	10037.1
		680	1.02027	Low confidence	11790.8	11556.6
	Squared	227	1.35551	High confidence	2253.78	1662.68
		800	1.00633	Low confidence	3485.53	3507.59
	Rooted	490	1.00094	High confidence	24.4079	24.4309
		802	1.00447	Low confidence	22.1318	22.2307
aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468]	Measured	441	1.02355	High confidence	6303	6158
		668		Low confidence
	Ranked	466	1.01446	High confidence	1521	1543
		730		Low confidence
	Squared	423	1.04765	High confidence	9403.03	8975.38
		665		Low confidence
	Rooted	466	1.0117	High confidence	79.3914	78.4729
		759		Low confidence
associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799]	Measured	139	1.31317	High confidence	561.038	736.737
		144	1.2878	Low confidence	965.202	749.494
	Ranked	278	1.08181	High confidence	10763.4	11644
		673	1.02194	Low confidence	12774.5	13054.8
	Squared	145	1.75162	High confidence	146.067	255.854
		152	1.52448	Low confidence	2121.73	1391.77
	Rooted	336	1.05386	High confidence	19.4823	20.5317
		385	1.08768	Low confidence	19.1534	17.6094
ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973]	Measured	216	1.18256	High confidence	14756	12478
		370	1.11824	Low confidence	11468.3	10255.7
	Ranked	62	1.28017		6438	5029
		74	1.29915	High confidence	8759.5	6742.5
	Squared	187	1.37067	Low confidence	70431.3	51384.7
		207	1.40685	High confidence	102814	73080.8
	Rooted	326	1.05854		88.8829	83.9673
		735	1.01454	Low confidence	82.5719	81.3882
atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]	Measured	477	1.00704	High confidence	429	426
		791		Low confidence
	Ranked	476	1.00888	High confidence	8329	8403
		766		Low confidence
	Squared	470	1.01413	High confidence	43.56	42.9529
		779		Low confidence
	Rooted	486	1.00351	High confidence	20.7123	20.6398
		808		Low confidence
atp-dependent clp protease atp-binding subunit clpx-like, mitochondrial precursor. [swissprot;acc:o76031]	Measured	377	1.05332	High confidence	931.405	884.254
		709	1.01662	Low confidence	2393.3	2354.18

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.