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	Value Type	Network Comparison Type	Interaction Map	Filtered	green	red	network_comparison

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Showing element 101 to 150 of 12912 in total

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

description	Rank	Value Type	green	red	network_comparison
26s protease regulatory subunit 8 (proteasome subunit p45) (thyroid hormone receptor interacting protein 1) (trip1) (msug1 protein) (tat-binding protein homolog 10) (tbp10) (p45/sug). [swissprot;acc:p47210]	1637	Ranked	199.408	202.358	1.01479
	1721	Squared	53788.1	59318.4	1.10282
	2059	Rooted	76.9113	74.9362	1.02636
	2651	Measured	9234.09	9150.44	1.00914
26s protease regulatory subunit s10b (proteasome subunit p42) (p44) (conserved atpase domain protein 44) (cadp44). [swissprot;acc:q92524]	1577		6349.04	5923.66	1.07181
	1630	Squared	30113.9	27176.8	1.10807
	1944	Rooted	64.5421	62.7515	1.02853
	2478	Ranked	216.801	216.177	1.00289
26s proteasome non-atpase regulatory subunit 1 (26s proteasome regulatory subunit s1) (26s proteasome subunit p112). [swissprot;acc:q99460]	1476	Squared	29969	26860.7	1.11572
	1883	Measured	6195.48	5826	1.06342
	2129	Rooted	63.5033	62.0038	1.02418
	2368	Ranked	219.434	218.555	1.00402
26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832]	1537	Squared	29419.4	26432.8	1.11299
	1609	Measured	6242.44	5826.74	1.07134
	2064	Rooted	63.8594	62.2279	1.02622
	2269	Ranked	218.627	217.419	1.00556
26s proteasome non-atpase regulatory subunit 11 (26s proteasome regulatory subunit s9) (26s proteasome regulatory subunit p44.5). [swissprot;acc:o00231]	1586	Squared	29677.3	26736.9	1.10998
	1592	Measured	6271.79	5853.1	1.07153
	2026	Rooted	63.9816	62.2803	1.02732
	2367	Ranked	218.475	217.589	1.00407
26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232]	1541	Squared	29539	26551.2	1.11253
	1579	Measured	6261.87	5842.44	1.07179
	2045	Rooted	63.9809	62.309	1.02683
	2316	Ranked	218.311	217.241	1.00493
26s proteasome non-atpase regulatory subunit 13 (26s proteasome regulatory subunit s11) (26s proteasome regulatory subunit p40.5). [swissprot;acc:q9unm6]	1570	Squared	29658.6	26688.8	1.11128
	1585	Measured	6278.32	5858.48	1.07166
	2038	Rooted	64.07	62.382	1.02706
	2329	Ranked	218.116	217.112	1.00462
26s proteasome non-atpase regulatory subunit 2 (26s proteasome regulatory subunit s2) (26s proteasome subunit p97) (tumor necrosis factor type 1 receptor associated protein 2) (55.11 protein). [swissprot;acc:q13200]	1241	Measured	6980.13	6436.19	1.08451
	1395	Rooted	68.0886	65.478	1.03987
	1538	Squared	34111.1	30653.9	1.11278
	2175	Ranked	208.808	210.209	1.00671
26s proteasome non-atpase regulatory subunit 3 (26s proteasome regulatory subunit s3) (proteasome subunit p58). [swissprot;acc:o43242]	1546	Measured	6244.37	5819.39	1.07303
	1548	Squared	29370.7	26408.9	1.11215
	1964	Rooted	63.9151	62.1627	1.02819
	2440	Ranked	218.376	217.645	1.00336
26s proteasome non-atpase regulatory subunit 4 (26s proteasome regulatory subunit s5a) (rpn10) (multiubiquitin chain binding protein) (antisecretory factor-1) (af) (asf). [swissprot;acc:p55036]	1432		225.468	220.987	1.02028
	1439	Squared	26757.8	23913	1.11896
	1979	Measured	5800.97	5475.74	1.05939
	2482	Rooted	61.1463	60.4511	1.0115
26s proteasome non-atpase regulatory subunit 6 (26s proteasome regulatory subunit s10) (p42a) (proteasome regulatory particle subunit p44s10). [swissprot;acc:q15008]	1396	Squared	30747.3	27408.7	1.12181
	1472	Measured	6435.42	5984.47	1.07535
	1915	Rooted	64.872	63.054	1.02883
	2432	Ranked	216.556	215.807	1.00347
26s proteasome non-atpase regulatory subunit 7 (26s proteasome regulatory subunit s12) (proteasome subunit p40) (mov34 protein homolog). [swissprot;acc:p51665]	1554	Squared	29622.1	26642.1	1.11185
	1571	Measured	6273.4	5851.64	1.07208
	2013	Rooted	64.0462	62.3398	1.02737
	2355	Ranked	218.162	217.232	1.00428
26s proteasome non-atpase regulatory subunit 8 (26s proteasome regulatory subunit s14) (p31). [swissprot;acc:p48556]	1536	Measured	6350.53	5916.05	1.07344
	1691	Squared	29916.8	27060.6	1.10555

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.