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	green	Filtered	Value Type	Network Comparison Type	Interaction Map	red	network_comparison

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Showing element 401 to 450 of 33156 in total

Filtered  : 1
Network Comparison Type  : Divided

description	Rank	green	Value Type	Interaction Map	red	network_comparison
28s ribosomal protein s26, mitochondrial precursor (mrp-s26) (mrp- s13). [swissprot;acc:q9byn8]	2082	66.1778	Rooted	High confidence	64.5014	1.02599
	2449	35032	Squared		33026.7	1.06072
	2617	42162.6		Low confidence	43757.4	1.03782
	2675	215.108	Ranked	High confidence	214.893	1.001
28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933]	407	260.544			239.75	1.08673
	659	47.9816	Rooted		51.7081	1.07767
	1662	15480.4	Squared		13992.7	1.10632
	2530	3788.42	Measured		3880.5	1.02431
	2844	41427.9	Squared	Low confidence	42943	1.03657
	3986	7792.73	Measured		7621.65	1.02245
	4585	71.3675	Rooted		69.8928	1.0211
	4992	206.342	Ranked		206.266	1.00037
3 beta-hydroxy-delta 5-c27-steroid oxidoreductase. [refseq;acc:nm_025193]	1079	42724.1	Squared		44737.4	1.04712
	1667	193.866	Ranked		197.872	1.02066
	2627	75.4487	Rooted		73.0199	1.03326
	3147	0.00001	Measured	High confidence	0.00001	1
			Ranked
			Squared
			Rooted
	3493	8292.57	Measured	Low confidence	8082.12	1.02604
3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8]	1073	42724.1	Squared		44737.4	1.04712
	1663	193.866	Ranked		197.872	1.02066
	2622	75.4487	Rooted		73.0199	1.03326
	2756	0.00001	Measured	High confidence	0.00001	1
			Ranked
			Squared
			Rooted
	3487	8292.57	Measured	Low confidence	8082.12	1.02604
3 beta-hydroxysteroid dehydrogenase/delta 5-->4-isomerase type i (3beta-hsd i) (trophoblast antigen fdo161g) [includes: 3-beta-hydroxy- delta(5)-steroid dehydrogenase (ec 1.1.1.145) (3-beta-hydroxy-5-ene steroid dehydrogenase) (progesterone reductase); steroid delta- isomerase (ec 5.3.3.1) (delta-5-3-ketosteroid isomerase)]. [swissprot;acc:p14060]	1075	42724.1	Squared		44737.4	1.04712
	1665	193.866	Ranked		197.872	1.02066
	2624	75.4487	Rooted		73.0199	1.03326
	2802	0.00001	Measured	High confidence	0.00001	1
			Ranked
			Squared
			Rooted
	3489	8292.57	Measured	Low confidence	8082.12	1.02604
3'(2'), 5'-bisphosphate nucleotidase 1; bisphosphate 3'-nucleotidase; bpntase; pap-inositol-1,4-phosphatase. [refseq;acc:nm_006085]	178	221.607	Ranked		209.954	1.0555
	2650	36053.6	Squared		37407.8	1.03756
	4603	65.5857	Rooted		66.9425	1.02069
	4994	6911.72	Measured		6922.79	1.0016
3'-5' rna exonuclease; polynucleotide phosphorylase-like. [refseq;acc:nm_033109]	1373	201.696	Ranked		206.13	1.02198
	1388	72.4192	Rooted		69.8381	1.03696
	2310	7838.4	Measured		7602.32	1.03105
	2740	41084.3	Squared		42607.1	1.03707
3-hydroxy-3-methylglutaryl-coenzyme a reductase (ec 1.1.1.34) (hmg-coa reductase). [swissprot;acc:p04035]	1118	31123.3		High confidence	27234.2	1.1428
	2302	7263.68	Measured		6946.6	1.04565
	2303	192.542	Ranked		191.567	1.00509
	2488	72.2598	Rooted		71.4412	1.01146
	3121	43211.7	Squared	Low confidence	44716.9	1.03483
	3261	196.642	Ranked		199.744	1.01577

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.