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	Network Comparison Type	Interaction Map	Filtered	green	red	network_comparison

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Showing element 501 to 550 of 33156 in total

Network Comparison Type  : Divided
Filtered  : 1

description	Rank	Value Type	Interaction Map	green	red	network_comparison
3-oxo-5-alpha-steroid 4-dehydrogenase 2 (ec 1.3.99.5) (steroid 5-alpha-reductase 2) (sr type 2) (5 alpha-sr2). [swissprot;acc:p31213]	950	Ranked	Low confidence	199.196	204.147	1.02485
	972	Rooted	High confidence	65.1892	61.6649	1.05715
	1084	Ranked		213.685	220.118	1.03011
	1143	Rooted	Low confidence	73.8482	71.1233	1.03831
	1275	Measured	High confidence	6371.14	5885	1.08261
	1627	Squared	Low confidence	43316.1	45165.2	1.04269
	2090	Measured		8138.17	7887.47	1.03178
	2610	Squared	High confidence	30015.7	28935	1.03735
3-oxo-5-beta-steroid 4-dehydrogenase (ec 1.3.99.6) (delta(4)-3- ketosteroid 5-beta-reductase) (aldo-keto reductase family 1 member d1). [swissprot;acc:p51857]	1902	Ranked	Low confidence	197.384	201.286	1.01977
	2018	Rooted		74.9328	72.3967	1.03503
	2235	Measured		8361.72	8107.73	1.03133
	3174	Squared		44839.4	46389.7	1.03457
3-phosphoinositide dependent protein kinase-1 (ec 2.7.1.37) (hpdk1). [swissprot;acc:o15530]	897	Ranked	High confidence	283.472	272.878	1.03882
	2394	Rooted		42.7253	43.4014	1.01582
	2513	Squared	Low confidence	42545.5	44180.9	1.03844
	2547	Measured	High confidence	3444.18	3370.46	1.02187
	2650	Squared		16197	16658.1	1.02847
	3553	Measured	Low confidence	7932.5	7733.78	1.0257
	4104	Rooted		71.9424	70.109	1.02615
	4765	Ranked		205.83	206.842	1.00492
38 kda fk-506 binding protein homolog (fkbpr38) (fk506-binding protein 8). [swissprot;acc:q14318]	116	Squared		45948.1	52687.3	1.14667
	1826	Rooted	High confidence	69.9589	67.8897	1.03048
	2068	Ranked	Low confidence	207.631	203.696	1.01932
	2261	Measured	High confidence	6786.23	6486.84	1.04615
	2358	Ranked		197.346	198.181	1.00423
	2710	Squared		28336.5	27920.7	1.01489
	3779	Measured	Low confidence	8198.63	8396.92	1.02419
	4988	Rooted		72.2334	72.4649	1.0032
4-aminobutyrate aminotransferase, mitochondrial precursor (ec 2.6.1.19) (gamma-amino-n-butyrate transaminase) (gaba transaminase) (gaba aminotransferase) (gaba-at) (gaba-t). [swissprot;acc:p80404]	696	Squared	High confidence	26693.1	22778.5	1.17186
	727	Measured	Low confidence	8803.2	8443.4	1.04261
	1469		High confidence	5887.45	5473.09	1.07571
	1579	Rooted	Low confidence	77.0332	74.3423	1.0362
	1745	Ranked	High confidence	222.215	219.423	1.01272
	2352	Rooted		61.9962	60.9091	1.01785
	2696	Ranked	Low confidence	193.541	196.941	1.01757
	4943	Squared		48349.1	48134.6	1.00446
4-hydroxyphenylpyruvate dioxygenase (ec 1.13.11.27) (4hppd) (hpd) (hppdase). [swissprot;acc:p32754]	1057	Rooted		74.502	71.724	1.03873
	1132	Measured		8336.19	8039.62	1.03689
	1159	Ranked		198.786	203.422	1.02332
	4625	Squared		45456.1	46235.3	1.01714
40 kda peptidyl-prolyl cis-trans isomerase (ec 5.2.1.8) (ppiase) (rotamase) (cyclophilin-40) (cyp-40) (cyclophilin-related protein). [swissprot;acc:q08752]	1110	Measured		8628.8	8320.39	1.03707
	2376	Rooted		76.2777	73.7734	1.03395
	3251	Ranked		194.871	197.955	1.01583
	4792	Squared		46667.2	47191.9	1.01124
40s ribosomal protein s10. [swissprot;acc:p46783]	2273			44372	46093.2	1.03879
	3069	Measured		8233.31	8010.65	1.0278
	3077	Rooted		74.0638	71.7722	1.03193
	3263	Ranked		199.593	202.739	1.01576
40s ribosomal protein s11. [swissprot;acc:p04643]	278		High confidence	267.088	241.399	1.10642
	335	Rooted		45.5342	50.4705	1.10841

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.