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

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Showing element 101 to 150 of 38536 in total

Network Comparison Type  : Divided

description	Filtered	Rank	green	Value Type	Interaction Map	network_comparison	red
14-3-3 protein zeta/delta (protein kinase c inhibitor protein-1) (kcip-1) (factor activating exoenzyme s) (fas). [swissprot;acc:p29312]	1	1961	63.0743	Rooted	High confidence	1.02824	61.3419
		2108	194.902	Ranked	Low confidence	1.01923	198.65
		2396	221.51		High confidence	1.00375	220.683
		4466	50905.5	Squared	Low confidence	1.02147	49835.4
14.5 kda translational inhibitor protein (p14.5) (uk114 antigen homolog). [swissprot;acc:p52758]		921	29768.2		High confidence	1.15651	25739.7
		927	74.7636	Rooted	Low confidence	1.0398	71.9022
		993	8288.57	Measured		1.03829	7982.87
		1044	196.966	Ranked		1.02415	201.723
		1600	6788.96	Measured	High confidence	1.07145	6336.22
		2036	68.7832	Rooted		1.02714	66.966
		2366	202.529	Ranked		1.00407	203.353
		4150	44213.2	Squared	Low confidence	1.02647	45383.4
15 kda selenoprotein precursor. [swissprot;acc:o60613]		914	34456.5		High confidence	1.15734	29772.1
		1043	6933.36	Measured		1.09283	6344.41
		1334	67.2624	Rooted		1.04128	64.5959
		1948	212.432	Ranked		1.00984	214.522
		2675	43157.8	Squared	Low confidence	1.03746	44774.4
		3577	8083.96	Measured		1.02563	7881.96
		3869	73.3413	Rooted		1.02822	71.3287
		4465	201.104	Ranked		1.00907	202.928
15-hydroxyprostaglandin dehydrogenase [nad(+)] (ec 1.1.1.141) (pgdh). [swissprot;acc:p15428]		2067	8425.81	Measured		1.03184	8165.8
		2855	0.00001		High confidence	1	0.00001
				Ranked
				Squared
				Rooted
		3576	75.5218		Low confidence	1.0298	73.3363
		4126	195.778	Ranked		1.01062	197.858
		4553	44651.1	Squared		1.01946	45519.8
16.7kd protein. [refseq;acc:nm_016139]		788	45775.4			1.05172	48142.9
		3267	195.864	Ranked		1.01575	198.949
		3651	75.5801	Rooted		1.02955	73.4106
		4005	8483.17	Measured		1.02235	8297.71
17 beta-hydroxysteroid dehydrogenase. [sptrembl;acc:q13034]		1051	217.998	Ranked	High confidence	1.03097	211.449
			8498.04	Measured	Low confidence	1.0377	8189.31
		1381	75.6999	Rooted		1.03702	72.9975
		1803	195.655	Ranked		1.02012	199.592
		2377	27574.1	Squared	High confidence	1.06837	25809.5
		2521	6113.96	Measured		1.02511	5964.17
		2642	63.5847	Rooted		1.00617	63.9773
		4655	45738.2	Squared	Low confidence	1.01655	46495
17-beta-hydroxysteroid dehydrogenase type vii-like. [refseq;acc:nm_182829]	0	627	10050.9	Ranked		1.02953	10347.7
		768	39.5126	Rooted		1.0106	39.0982
		778	4869.42	Measured		1.00902	4825.89
		815	40451	Squared		1.00447	40270.8
	1	631	8689.28	Measured		1.04487	8316.12
		1116	76.9933	Rooted		1.03844	74.1433
		2142	192.884	Ranked		1.01915	196.577
		4933	45903.5	Squared		1.00521	46142.7
2,4-dienoyl coa reductase 2, peroxisomal; peroxisomal 2,4-dienoyl-coa reductase. [refseq;acc:nm_020664]		447	45146.7			1.06579	48116.9
		3846	198.422	Ranked		1.01306	201.014

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.