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

Results: HTML CSV LaTeX

Showing element 401 to 450 of 14920 in total

Network Comparison Type  : Divided
Interaction Map  : High confidence

description	Rank	Value Type	Filtered	red	network_comparison	green
40s ribosomal protein s5. [swissprot;acc:p46782]	366	Ranked	1	242.473	1.09602	265.756
	467	Rooted		50.4649	1.09446	46.1093
	1820	Squared		13022.7	1.09738	14290.8
	2343	Measured		3672.17	1.04413	3516.98
40s ribosomal protein s7 (s8). [swissprot;acc:p23821]	1561	Squared		26174.3	1.11172	29098.4
	1642	Measured		5782.92	1.06977	6186.39
	2102	Rooted		61.9958	1.02489	63.5389
	2149	Ranked		217.871	1.00686	219.366
40s ribosomal protein s8. [swissprot;acc:p09058]	1213	Rooted		61.4774	1.04598	64.3044
	1397	Ranked		218.64	1.02145	214.049
	1471	Measured		5659.45	1.07564	6087.55
	2111	Squared		24799.3	1.08812	26984.5
40s ribosomal protein s9. [swissprot;acc:p46781]	439	Ranked		238.986	1.07866	257.784
	786	Rooted		52.0101	1.0655	48.813
	1746	Squared		14357.1	1.10056	15800.8
	2628	Measured		3933.74	1.0146	3877.14
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]	259	Rooted	0	21.9471	1.10389	19.8816
	298	Ranked		11977.8	1.07219	12842.5
	315	Measured		1212.82	1.09796	1104.61
	411	Squared		2967.63	1.05865	3141.67
	789	Ranked	1	224.244	1.04578	234.511
	1047	Squared		20357.7	1.14717	23353.8
	2380	Rooted		58.6893	1.01623	57.7518
	2402	Measured		5078.5	1.03884	5275.76
43 kda receptor-associated protein of the synapse (rapsyn) (acetylcholine receptor-associated 43 kda protein) (43 kda postsynaptic protein). [swissprot;acc:q13702]	1402			6160.06	1.07804	6640.78
	1514	Rooted		63.609	1.03698	65.9615
	1601	Squared		29238.6	1.10929	32434.1
	2232	Ranked		215.547	1.00632	214.194
44050 protein. [refseq;acc:nm_178832]	130	Squared		148058	1.4861	99628.4
	376	Measured		17385.9	1.16769	14889.2
	1193	Rooted		108.34	1.04675	103.501
	2506	Ranked		151.386	1.0025	151.009
45 kda calcium-binding protein precursor (cab45) (stromal cell-derived factor 4) (sdf-4). [swissprot;acc:q9brk5]	375	Squared		45987	1.23463	56777.1
	972	Measured		7813.48	1.09684	8570.11
	1733	Rooted		70.2391	1.03208	72.4922
	2147	Ranked		206.442	1.00688	207.862
5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478]	600	Squared		34129.6	1.18473	40434.5
	691	Measured		6920.69	1.11949	7747.63
	755	Rooted		66.9737	1.06704	71.4637
	879	Ranked		212.002	1.03946	203.954
5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741]	598	Squared		34129.6	1.18473	40434.5
	689	Measured		6920.69	1.11949	7747.63
	753	Rooted		66.9737	1.06704	71.4637
	877	Ranked		212.002	1.03946	203.954
5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131]	597	Squared		34129.4	1.18473	40434.2
	688	Measured		6920.67	1.11949	7747.6
	752	Rooted		66.9736	1.06704	71.4636
	876	Ranked		212.002	1.03946	203.954
5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646]	595	Squared		34129.7	1.18474	40434.8
	687	Measured		6920.71	1.11949	7747.65

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.