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	Filtered	Network Comparison Type	red	network_comparison	green

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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	network_comparison	green
26s protease regulatory subunit 6b (mip224) (mb67 interacting protein) (tat-binding protein-7) (tbp-7). [swissprot;acc:p43686]	1489	Squared	1	26277.3	1.115	29299.3
	1567	Measured		5822.25	1.07226	6242.94
	2044	Rooted		62.2342	1.02686	63.9055
	2327	Ranked		217.413	1.00466	218.426
26s protease regulatory subunit 7 (mss1 protein). [swissprot;acc:p35998]	1481	Squared		26142.6	1.11557	29163.8
	1539	Measured		5783.97	1.07322	6207.5
	1979	Rooted		61.9542	1.02776	63.6738
	2395	Ranked		218.192	1.00377	219.014
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	1.01479	199.408
	1721	Squared		59318.4	1.10282	53788.1
	2059	Rooted		74.9362	1.02636	76.9113
	2651	Measured		9150.44	1.00914	9234.09
26s protease regulatory subunit s10b (proteasome subunit p42) (p44) (conserved atpase domain protein 44) (cadp44). [swissprot;acc:q92524]	1577			5923.66	1.07181	6349.04
	1630	Squared		27176.8	1.10807	30113.9
	1944	Rooted		62.7515	1.02853	64.5421
	2478	Ranked		216.177	1.00289	216.801
26s proteasome non-atpase regulatory subunit 1 (26s proteasome regulatory subunit s1) (26s proteasome subunit p112). [swissprot;acc:q99460]	1476	Squared		26860.7	1.11572	29969
	1883	Measured		5826	1.06342	6195.48
	2129	Rooted		62.0038	1.02418	63.5033
	2368	Ranked		218.555	1.00402	219.434
26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832]	316	Squared	0	8620.27	1.17196	7355.46
	370	Rooted		30.7424	1.04188	32.0298
	379	Ranked		11228.4	1.03909	10806
	451	Measured		2683.61	1.01545	2642.79
	1537	Squared	1	26432.8	1.11299	29419.4
	1609	Measured		5826.74	1.07134	6242.44
	2064	Rooted		62.2279	1.02622	63.8594
	2269	Ranked		217.419	1.00556	218.627
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	1.10998	29677.3
	1592	Measured		5853.1	1.07153	6271.79
	2026	Rooted		62.2803	1.02732	63.9816
	2367	Ranked		217.589	1.00407	218.475
26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232]	328	Squared	0	6747.71	1.14785	5878.56
	458	Rooted		28.0847	1.01531	28.5146
	474	Measured		2281.12	1.00763	2263.85
	495	Ranked		11725.2	1.00195	11748.1
	1541	Squared	1	26551.2	1.11253	29539
	1579	Measured		5842.44	1.07179	6261.87
	2045	Rooted		62.309	1.02683	63.9809
	2316	Ranked		217.241	1.00493	218.311
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	1.11128	29658.6
	1585	Measured		5858.48	1.07166	6278.32
	2038	Rooted		62.382	1.02706	64.07
	2329	Ranked		217.112	1.00462	218.116
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	1.08451	6980.13
	1395	Rooted		65.478	1.03987	68.0886
	1538	Squared		30653.9	1.11278	34111.1
	2175	Ranked		210.209	1.00671	208.808
26s proteasome non-atpase regulatory subunit 3 (26s proteasome regulatory subunit s3) (proteasome subunit p58). [swissprot;acc:o43242]	1546	Measured		5819.39	1.07303	6244.37
	1548	Squared		26408.9	1.11215	29370.7

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.