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

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Showing element 501 to 550 of 12912 in total

Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1

description	green	Value Type	Rank	red	network_comparison
60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914]	45.6718	Rooted	387	50.3345	1.10209
	266.673	Ranked	306	242.153	1.10126
	3423.89	Measured	2074	3614.91	1.05579
	13562.6	Squared	2003	12429.9	1.09113
60s ribosomal protein l15. [swissprot;acc:p39030]	57.9477	Rooted	2238	59.1718	1.02112
	230.978	Ranked	604	217.862	1.0602
	5006.1	Measured	2532	4888.72	1.02401
	20351.7	Squared	1089	17766.4	1.14552
60s ribosomal protein l17 (l23). [swissprot;acc:p18621]	45.4333	Rooted	343	50.3169	1.10749
	267.335	Ranked	281	241.808	1.10557
	3384.59	Measured	1894	3598.08	1.06308
	13390.2	Squared	2212	12360.4	1.08331
60s ribosomal protein l18. [swissprot;acc:q07020]	50.0947	Rooted	969	52.9804	1.0576
	254.667	Ranked	485	237.109	1.07405
	4095.53	Measured	2694	4113.79	1.00446
	17067.9	Squared	1618	15399.5	1.10834
60s ribosomal protein l18a. [swissprot;acc:q02543]	59.3786	Rooted	770	55.6817	1.06639
	224.958	Ranked	860	234.025	1.04031
	5226.71	Measured	806	4708.61	1.11003
	21540.4	Squared	1128	18854.4	1.14246
60s ribosomal protein l19. [swissprot;acc:p14118]	46.3081	Rooted	435	50.832	1.09769
	264.729	Ranked	319	240.73	1.09969
	3499.2	Measured	2136	3687.49	1.05381
	13918.3	Squared	2054	12769	1.09001
60s ribosomal protein l21. [swissprot;acc:p46778]	63.2237	Rooted	1051	60.1366	1.05133
	217.263	Ranked	1054	223.958	1.03082
	5957.99	Measured	1510	5546.11	1.07426
	26738.9	Squared	2453	25226.2	1.05997
60s ribosomal protein l22 (epstein-barr virus small rna associated protein) (eber associated protein) (eap) (heparin binding protein hbp15). [swissprot;acc:p35268]	72.5201	Rooted	2667	72.1844	1.00465
	200.413	Ranked	2205	199.129	1.00645
	7741.14	Measured	2673	7780.98	1.00515
	36568.4	Squared	2530	38544.3	1.05403
60s ribosomal protein l23 (l17). [swissprot;acc:p23131]	46.0607	Rooted	384	50.7723	1.10229
	265.717	Ranked	293	240.782	1.10356
	3482.34	Measured	2115	3672.49	1.0546
	13887.8	Squared	1838	12666.8	1.09639
60s ribosomal protein l23a. [swissprot;acc:p29316]	45.9373	Rooted	424	50.4703	1.09868
	265.945	Ranked	323	241.884	1.09947
	3463.88	Measured	2175	3642.13	1.05146
	13806.3	Squared	1950	12632.4	1.09293
60s ribosomal protein l24 (l30). [swissprot;acc:p38663]	73.3177	Rooted	1128	69.8977	1.04893
	198.86	Ranked	1767	201.288	1.01221
	7911.25	Measured	727	7087.23	1.11627
	37652.3	Squared	420	30924.3	1.21756
60s ribosomal protein l26. [swissprot;acc:q02877]	45.5599	Rooted	374	50.2549	1.10305
	267.008	Ranked	302	242.326	1.10185
	3409.48	Measured	2051	3601.97	1.05646
	13513	Squared	1997	12380.1	1.09151
60s ribosomal protein l28. [swissprot;acc:p46779]	65.4287	Rooted	1506	63.0816	1.03721
	213.61	Ranked	1882	215.896	1.0107

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.