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

Results: HTML CSV LaTeX

Showing element 12864 to 12913 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

description	Rank	Network Comparison Type	Value Type	green	red	network_comparison
megf6 (fragment). [sptrembl;acc:o75095]	1756	Divided	Ranked	219.09	221.811	1.01242
megsin (tp55) (serpin b7). [swissprot;acc:o75635]	1643	Subtracted	Squared	28767.6	26276.4	2491.2
	1688	Divided	Measured	6165.87	5767.69	1.06904
	1714	Subtracted				398.18
	1881	Divided	Squared	28767.6	26276.4	1.09481
	1987		Rooted	63.5621	61.8616	1.02749
	2018	Subtracted				1.7005
	2402		Ranked	218.984	218.2	0.784
	2414	Divided				1.00359
meiotic recombination protein dmc1/lim15 homolog. [swissprot;acc:q14565]	687		Squared	28893.6	24633.6	1.17293
	720	Subtracted				4260
	1153		Measured	6423.98	5913.73	510.25
	1208	Divided				1.08628
	1936	Subtracted	Rooted	65.3899	63.5764	1.8135
	1947	Divided				1.02852
	2255	Subtracted	Ranked	214.606	213.391	1.215
	2259	Divided				1.00569
meiotic recombination protein spo11. [swissprot;acc:q9y5k1]	844	Subtracted		245.547	236.741	8.806
	924	Divided				1.0372
	2314		Squared	17167.1	15947.3	1.07649
	2347		Rooted	52.3236	53.2692	1.01807
	2400	Subtracted				0.9456
	2450		Squared	17167.1	15947.3	1219.8
	2588	Divided	Measured	4253.46	4180.32	1.0175
	2632	Subtracted				73.14
melanoma antigen p15 (melanoma-associated antigen recognized by t lymphocytes). [swissprot;acc:q13084]	804		Ranked	221.785	212.386	9.399
	816	Divided				1.04425
	2210		Rooted	61.0748	62.412	1.02189
	2277	Subtracted				1.3372
	2642		Squared	24679.6	24123.5	556.1
	2687	Divided				1.02305
	2718	Subtracted	Measured	5583.64	5603.24	19.6
	2727	Divided				1.00351
melanoma antigen recognized by t cells 2. [refseq;acc:nm_018194]	622	Subtracted	Squared	31927.7	27407.7	4520
	790	Divided				1.16492
	1582	Subtracted	Measured	7287.27	6858.84	428.43
	1914	Divided				1.06246
	2257	Subtracted	Rooted	71.8706	70.5239	1.3467
	2316	Divided				1.0191
	2495		Ranked	195.08	194.527	1.00284
	2506	Subtracted				0.553
melanoma antigen, family b, 6. [refseq;acc:nm_173523]	20		Squared	129762	219048	89286
	31		Measured	18263	23693.7	5430.7
	56		Rooted	120.823	137.446	16.623
	64	Divided	Squared	129762	219048	1.68808
	93		Ranked	110.265	88.2482	1.24949
	162		Measured	18263	23693.7	1.29736
	233		Rooted	120.823	137.446	1.13758
	311	Subtracted	Ranked	110.265	88.2482	22.0168
melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	10		Squared	129762	219048	89286

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.