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

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Showing element 401 to 450 of 14920 in total

Network Comparison Type  : Divided
Interaction Map  : High confidence

description	Value Type	Rank	Filtered	red	network_comparison	green
40s ribosomal protein s5. [swissprot;acc:p46782]	Measured	2343	1	3672.17	1.04413	3516.98
	Ranked	366		242.473	1.09602	265.756
	Squared	1820		13022.7	1.09738	14290.8
	Rooted	467		50.4649	1.09446	46.1093
40s ribosomal protein s7 (s8). [swissprot;acc:p23821]	Measured	1642		5782.92	1.06977	6186.39
	Ranked	2149		217.871	1.00686	219.366
	Squared	1561		26174.3	1.11172	29098.4
	Rooted	2102		61.9958	1.02489	63.5389
40s ribosomal protein s8. [swissprot;acc:p09058]	Measured	1471		5659.45	1.07564	6087.55
	Ranked	1397		218.64	1.02145	214.049
	Squared	2111		24799.3	1.08812	26984.5
	Rooted	1213		61.4774	1.04598	64.3044
40s ribosomal protein s9. [swissprot;acc:p46781]	Measured	2628		3933.74	1.0146	3877.14
	Ranked	439		238.986	1.07866	257.784
	Squared	1746		14357.1	1.10056	15800.8
	Rooted	786		52.0101	1.0655	48.813
40s ribosomal protein sa (p40) (34/67 kda laminin receptor) (colon carcinoma laminin-binding protein) (nem/1chd4) (multidrug resistance- associated protein mgr1-ag). [swissprot;acc:p08865]	Measured	315	0	1212.82	1.09796	1104.61
		2402	1	5078.5	1.03884	5275.76
	Ranked	298	0	11977.8	1.07219	12842.5
		789	1	224.244	1.04578	234.511
	Squared	411	0	2967.63	1.05865	3141.67
		1047	1	20357.7	1.14717	23353.8
	Rooted	259	0	21.9471	1.10389	19.8816
		2380	1	58.6893	1.01623	57.7518
43 kda receptor-associated protein of the synapse (rapsyn) (acetylcholine receptor-associated 43 kda protein) (43 kda postsynaptic protein). [swissprot;acc:q13702]	Measured	1402		6160.06	1.07804	6640.78
	Ranked	2232		215.547	1.00632	214.194
	Squared	1601		29238.6	1.10929	32434.1
	Rooted	1514		63.609	1.03698	65.9615
44050 protein. [refseq;acc:nm_178832]	Measured	376		17385.9	1.16769	14889.2
	Ranked	2506		151.386	1.0025	151.009
	Squared	130		148058	1.4861	99628.4
	Rooted	1193		108.34	1.04675	103.501
45 kda calcium-binding protein precursor (cab45) (stromal cell-derived factor 4) (sdf-4). [swissprot;acc:q9brk5]	Measured	972		7813.48	1.09684	8570.11
	Ranked	2147		206.442	1.00688	207.862
	Squared	375		45987	1.23463	56777.1
	Rooted	1733		70.2391	1.03208	72.4922
5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478]	Measured	691		6920.69	1.11949	7747.63
	Ranked	879		212.002	1.03946	203.954
	Squared	600		34129.6	1.18473	40434.5
	Rooted	755		66.9737	1.06704	71.4637
5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741]	Measured	689		6920.69	1.11949	7747.63
	Ranked	877		212.002	1.03946	203.954
	Squared	598		34129.6	1.18473	40434.5
	Rooted	753		66.9737	1.06704	71.4637
5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131]	Measured	688		6920.67	1.11949	7747.6
	Ranked	876		212.002	1.03946	203.954
	Squared	597		34129.4	1.18473	40434.2
	Rooted	752		66.9736	1.06704	71.4636
5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646]	Measured	687		6920.71	1.11949	7747.65
	Ranked	875		212.002	1.03946	203.954

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.