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

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Showing element 151 to 200 of 14920 in total

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

description	Rank	Value Type	green	red	network_comparison
26s proteasome non-atpase regulatory subunit 3 (26s proteasome regulatory subunit s3) (proteasome subunit p58). [swissprot;acc:o43242]	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
	1861	Rooted	64.64	62.7784	1.02965
	2525	Ranked	216.341	215.835	1.00234
26s proteasome non-atpase regulatory subunit 9 (26s proteasome regulatory subunit p27). [swissprot;acc:o00233]	1517	Measured	6439.46	5996.14	1.07393
	1628	Squared	30763.9	27762.4	1.10811
	1831	Rooted	64.9964	63.0811	1.03036
	2620	Ranked	215.91	215.615	1.00137
26s proteasome-associated pad1 homolog. [refseq;acc:nm_005805]	1562	Squared	29098.4	26174.3	1.11172
	1643	Measured	6186.39	5782.92	1.06977
	2103	Rooted	63.5389	61.9958	1.02489
	2150	Ranked	219.366	217.871	1.00686
27 kda golgi snare protein (golgi snap receptor complex member 2) (membrin). [swissprot;acc:o14653]	810		221.785	212.386	1.04425
	2204	Rooted	61.0748	62.412	1.02189
	2681	Squared	24679.6	24123.5	1.02305
	2720	Measured	5583.64	5603.24	1.00351
28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235]	325	Ranked	268.195	243.944	1.09941
	383	Rooted	45.2077	49.8325	1.1023
	1966	Squared	13441.9	12300.5	1.09279
	2153	Measured	3381.34	3560.63	1.05302
28s ribosomal protein s16, mitochondrial precursor (mrp-s16) (cgi- 132). [swissprot;acc:q9y3d3]	1409	Squared	24115.7	21512.7	1.121
	1955	Measured	5510.67	5195.3	1.0607
	2212	Ranked	225.854	224.411	1.00643
	2305	Rooted	60.1552	59.0186	1.01926
28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	23	Ranked	44	58	1.31818
	35	Squared	192141	106226	1.80879
	115	Measured	28492	21185	1.34491
	173	Rooted	168.796	145.551	1.1597
28s ribosomal protein s18a, mitochondrial precursor (mrp-s18-a) (mrps18a) (mrp-s18-3). [swissprot;acc:q9nvs2]	828	Squared	28112.8	24211.7	1.16112
	835	Measured	6218.77	5623.18	1.10592
	1149	Rooted	64.5415	61.5672	1.04831
	1659	Ranked	214.826	217.925	1.01443
28s ribosomal protein s26, mitochondrial precursor (mrp-s26) (mrp- s13). [swissprot;acc:q9byn8]	2071	Measured	6797.24	6437.24	1.05592
	2082	Rooted	66.1778	64.5014	1.02599
	2449	Squared	35032	33026.7	1.06072
	2675	Ranked	215.108	214.893	1.001

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.