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	Interaction Map	Network Comparison Type	Filtered	red	green	network_comparison

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Showing element 101 to 150 of 14920 in total

Interaction Map  : High confidence
Network Comparison Type  : Divided

description	Rank	Value Type	Filtered	red	green	network_comparison
26s protease regulatory subunit 6b (mip224) (mb67 interacting protein) (tat-binding protein-7) (tbp-7). [swissprot;acc:p43686]	1489	Squared	1	26277.3	29299.3	1.115
	1567	Measured		5822.25	6242.94	1.07226
	2044	Rooted		62.2342	63.9055	1.02686
	2327	Ranked		217.413	218.426	1.00466
26s protease regulatory subunit 7 (mss1 protein). [swissprot;acc:p35998]	1481	Squared		26142.6	29163.8	1.11557
	1539	Measured		5783.97	6207.5	1.07322
	1979	Rooted		61.9542	63.6738	1.02776
	2395	Ranked		218.192	219.014	1.00377
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			202.358	199.408	1.01479
	1721	Squared		59318.4	53788.1	1.10282
	2059	Rooted		74.9362	76.9113	1.02636
	2651	Measured		9150.44	9234.09	1.00914
26s protease regulatory subunit s10b (proteasome subunit p42) (p44) (conserved atpase domain protein 44) (cadp44). [swissprot;acc:q92524]	1577			5923.66	6349.04	1.07181
	1630	Squared		27176.8	30113.9	1.10807
	1944	Rooted		62.7515	64.5421	1.02853
	2478	Ranked		216.177	216.801	1.00289
26s proteasome non-atpase regulatory subunit 1 (26s proteasome regulatory subunit s1) (26s proteasome subunit p112). [swissprot;acc:q99460]	1476	Squared		26860.7	29969	1.11572
	1883	Measured		5826	6195.48	1.06342
	2129	Rooted		62.0038	63.5033	1.02418
	2368	Ranked		218.555	219.434	1.00402
26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832]	316	Squared	0	8620.27	7355.46	1.17196
	370	Rooted		30.7424	32.0298	1.04188
	379	Ranked		11228.4	10806	1.03909
	451	Measured		2683.61	2642.79	1.01545
	1537	Squared	1	26432.8	29419.4	1.11299
	1609	Measured		5826.74	6242.44	1.07134
	2064	Rooted		62.2279	63.8594	1.02622
	2269	Ranked		217.419	218.627	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		26736.9	29677.3	1.10998
	1592	Measured		5853.1	6271.79	1.07153
	2026	Rooted		62.2803	63.9816	1.02732
	2367	Ranked		217.589	218.475	1.00407
26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232]	328	Squared	0	6747.71	5878.56	1.14785
	458	Rooted		28.0847	28.5146	1.01531
	474	Measured		2281.12	2263.85	1.00763
	495	Ranked		11725.2	11748.1	1.00195
	1541	Squared	1	26551.2	29539	1.11253
	1579	Measured		5842.44	6261.87	1.07179
	2045	Rooted		62.309	63.9809	1.02683
	2316	Ranked		217.241	218.311	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		26688.8	29658.6	1.11128
	1585	Measured		5858.48	6278.32	1.07166
	2038	Rooted		62.382	64.07	1.02706
	2329	Ranked		217.112	218.116	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		6436.19	6980.13	1.08451
	1395	Rooted		65.478	68.0886	1.03987
	1538	Squared		30653.9	34111.1	1.11278
	2175	Ranked		210.209	208.808	1.00671
26s proteasome non-atpase regulatory subunit 3 (26s proteasome regulatory subunit s3) (proteasome subunit p58). [swissprot;acc:o43242]	1546	Measured		5819.39	6244.37	1.07303
	1548	Squared		26408.9	29370.7	1.11215

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.