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

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Showing element 1 to 50 of 14920 in total

Filtered  : 0
Network Comparison Type  : Divided
Interaction Map  : High confidence

description	Rank	green	red	Value Type	network_comparison
1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	37	934.348	334.401	Measured	2.79409
		1034.13	101.05	Squared	10.2338
	53	18.0183	11.844	Rooted	1.5213
	242	13895.8	15260.6	Ranked	1.09822
25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [swissprot;acc:o15528]	19	26.1599	305.45	Measured	11.6763
	26	0.344399	44.3683	Squared	128.828
		3.80565	13.7805	Rooted	3.62106
	47	18499.2	12941.7	Ranked	1.42943
26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832]	316	7355.46	8620.27	Squared	1.17196
	370	32.0298	30.7424	Rooted	1.04188
	379	10806	11228.4	Ranked	1.03909
	451	2642.79	2683.61	Measured	1.01545
26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232]	328	5878.56	6747.71	Squared	1.14785
	458	28.5146	28.0847	Rooted	1.01531
	474	2263.85	2281.12	Measured	1.00763
	495	11748.1	11725.2	Ranked	1.00195
3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8]	299	11512.3	12338.7		1.07178
	438	44.9836	43.8864	Rooted	1.025
	492	5046.33	5038.33	Measured	1.00159
	493	17901.1	17901.1	Squared	1
3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362]	327	10466.5	9897.29	Ranked	1.05751
	376	31.1453	32.3671	Rooted	1.03923
	438	2853.65	2925.57	Measured	1.0252
	477	18218.3	18353.1	Squared	1.0074
3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [swissprot;acc:p09110]	346	1721.76	1837.26	Measured	1.06708
	357	26.8141	28.0711	Rooted	1.04688
	455	6794.39	6970.13	Squared	1.02587
	478	10243.1	10156.4	Ranked	1.00854
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]	36	2.18581	4.30525	Rooted	1.96964
	121	14.3333	19.6667	Measured	1.3721
	232	0.145878	0.108639	Squared	1.34278
	369	19704.7	18849.7	Ranked	1.04536
40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174]	222	11013.2	12183		1.10622
	251	23.5833	21.3142	Rooted	1.10646
	258	1337.54	1183.16	Measured	1.13048
	270	3201.81	2569.37	Squared	1.24615
40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]	186	10592.8	11935.1	Ranked	1.12672
	222	1735.23	1499.4	Measured	1.15728
	225	26.17	23.1768	Rooted	1.12915
	241	6172.1	4734.34	Squared	1.30369
40s ribosomal protein s26. [swissprot;acc:p02383]	43	5.66499	9.92134	Rooted	1.75134
	58	81.2233	150.741	Measured	1.85588
	112	17098	14269.7	Ranked	1.1982
	152	5.24885	8.80383	Squared	1.67729
40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677]	380	9936.37	9566.15	Ranked	1.0387
	395	30.9731	32.0326	Rooted	1.03421
	444	2378.99	2431.87	Measured	1.02223
	472	6524	6605.9	Squared	1.01255
40s ribosomal protein s28. [swissprot;acc:p25112]	258	14193.6	12967.1	Ranked	1.09459
	285	12.5026	13.5612	Rooted	1.08467

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.