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

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description	Rank	Network Comparison Type	Value Type	Hugo	Interaction Map	red	green	network_comparison
26s proteasome non-atpase regulatory subunit 1 (26s proteasome regulatory subunit s1) (26s proteasome subunit p112). [swissprot;acc:q99460]	2355	Subtracted	Ranked	PSMD1	High confidence	218.555	219.434	0.879
	2368	Divided						1.00402
	2447		Measured		Low confidence	7825.14	8063.51	1.03046
	2527	Subtracted						238.37
26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832]	1249		Squared	PSMD10	High confidence	26432.8	29419.4	2986.6
	1537	Divided						1.11299
	1609		Measured			5826.74	6242.44	1.07134
	1646	Subtracted						415.7
	1884				Low confidence	8137.96	8397.56	259.6
	2056	Divided						1.0319
	2061	Subtracted	Rooted		High confidence	62.2279	63.8594	1.6315
	2064	Divided						1.02622
	2256	Subtracted	Ranked			217.419	218.627	1.208
	2269	Divided						1.00556
	2566	Subtracted	Rooted		Low confidence	72.7032	75.1187	2.4155
	2649	Divided						1.03322
	3038		Ranked			200.303	197.031	1.01661
	3047	Subtracted						3.272
	4026		Squared			46258.5	45056.5	1202
	4141	Divided						1.02668
26s proteasome non-atpase regulatory subunit 11 (26s proteasome regulatory subunit s9) (26s proteasome regulatory subunit p44.5). [swissprot;acc:o00231]	744	Subtracted	Measured	PSMD11		8393.58	8727.99	334.41
	889	Divided						1.03984
	1278	Subtracted	Squared		High confidence	26736.9	29677.3	2940.4
	1282		Rooted		Low confidence	74.0544	76.7559	2.7015
	1508	Divided						1.03648
	1586		Squared		High confidence	26736.9	29677.3	1.10998
	1592		Measured			5853.1	6271.79	1.07153
	1634	Subtracted						418.69
	2016		Rooted			62.2803	63.9816	1.7013
	2026	Divided						1.02732
	2174		Ranked		Low confidence	197.69	193.995	1.01905
	2274	Subtracted						3.695
	2353				High confidence	217.589	218.475	0.886
	2367	Divided						1.00407
	4818	Subtracted	Squared		Low confidence	47846.2	47445.6	400.6
	4838	Divided						1.00844
26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232]	933	Subtracted	Measured	no value		8358.82	8671.34	312.52
	1073	Divided						1.03739
	1248	Subtracted	Squared		High confidence	26551.2	29539	2987.8
	1541	Divided						1.11253
	1579		Measured			5842.44	6261.87	1.07179
	1633	Subtracted						419.43
	2042		Rooted			62.309	63.9809	1.6719
	2045	Divided						1.02683
	2154	Subtracted			Low confidence	73.7276	76.2257	2.4981
	2300		Ranked		High confidence	217.241	218.311	1.07
	2316	Divided						1.00493
	2398		Rooted		Low confidence	73.7276	76.2257	1.03388
	3393		Ranked			198.522	195.526	1.01532
	3428	Subtracted						2.996

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
- Hugo is the HGNC identifier if it exists
- 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.