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

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Showing element 601 to 650 of 33156 in total

Filtered  : 1
Network Comparison Type  : Divided

description	Rank	green	Value Type	Interaction Map	red	network_comparison
40s ribosomal protein s17. [swissprot;acc:p08708]	1630	200.265	Ranked	Low confidence	204.428	1.02079
	1647	73.5316	Rooted		70.9771	1.03599
	2178	43088.4	Squared		44779.1	1.03924
	2603	8094.51	Measured		7859.39	1.02992
40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232]	387	264.11	Ranked	High confidence	242.238	1.09029
	531	46.6413	Rooted		50.6537	1.08603
	798	39783.7	Squared	Low confidence	41825.9	1.05133
	1824	14424.1		High confidence	13145.4	1.09727
	2309	211.63	Ranked	Low confidence	207.747	1.01869
	2437	3584.47	Measured	High confidence	3708.67	1.03465
	4873	7489.39		Low confidence	7428.65	1.00818
	4963	69.3391	Rooted		68.9337	1.00588
40s ribosomal protein s19. [swissprot;acc:p39019]	771	59.3786		High confidence	55.6817	1.06639
	807	5226.71	Measured		4708.61	1.11003
	861	224.958	Ranked		234.025	1.04031
	1129	21540.4	Squared		18854.4	1.14246
	1783	8192.82	Measured	Low confidence	7931.64	1.03293
	2264	73.9584	Rooted		71.5043	1.03432
	2888	199.442	Ranked		202.851	1.01709
	3998	44019.1	Squared		45258.8	1.02816
40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]	344	265.136	Ranked	High confidence	241.625	1.0973
	461	46.2239	Rooted		50.6156	1.09501
	1588	40413.3	Squared	Low confidence	42147.6	1.04291
	1954	13977.2		High confidence	12789.3	1.09288
	2242	3504.91	Measured		3670.45	1.04723
	4594	7628.91		Low confidence	7502.38	1.01687
	4600	208.423	Ranked		206.929	1.00722
	4792	70.456	Rooted		69.356	1.01586
40s ribosomal protein s20. [swissprot;acc:p17075]	342	267.21	Ranked	High confidence	243.5	1.09737
	425	45.5318	Rooted		50.0161	1.09849
	1926	13619.9	Squared		12452.6	1.09374
	2211	3422.6	Measured		3590.56	1.04907
	2240	40860.1	Squared	Low confidence	42451	1.03894
	4130	7691.51	Measured		7532.53	1.02111
	4617	70.8006	Rooted		69.3824	1.02044
	4957	207.585	Ranked		207.359	1.00109
40s ribosomal protein s21. [swissprot;acc:p35265]	790	234.511		High confidence	224.244	1.04578
	1048	23353.8	Squared		20357.7	1.14717
	2381	57.7518	Rooted		58.6893	1.01623
	2403	5275.76	Measured		5078.5	1.03884
	2816	43338.7	Squared	Low confidence	44925.9	1.03662
	3075	8144.7	Measured		7924.59	1.02778
	3413	73.7722	Rooted		71.5866	1.03053
	3794	199.787	Ranked		202.443	1.01329
40s ribosomal protein s23. [swissprot;acc:p39028]	324	268.195		High confidence	243.944	1.09941
	382	45.2077	Rooted		49.8325	1.1023
	1949	39598.2	Squared	Low confidence	41205.7	1.0406
	1965	13441.9		High confidence	12300.5	1.09279
	2152	3381.34	Measured		3560.63	1.05302
	4531	211.088	Ranked	Low confidence	209.371	1.0082

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.