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	Filtered	Interaction Map	Value Type	green	red	network_comparison	Network Comparison Type

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Showing element 3180 to 3229 of 38536 in total

Filtered  : 1
Network Comparison Type  : Divided

description	Rank	Interaction Map	Value Type	green	red	network_comparison
aminoacylase-1 (ec 3.5.1.14) (n-acyl-l-amino-acid amidohydrolase) (acy-1). [swissprot;acc:q03154]	724	Low confidence	Ranked	196.371	201.765	1.02747
	1420	High confidence		208.229	203.979	1.02084
	2349		Measured	8001.45	8353.97	1.04406
	2479		Rooted	71.2783	72.1147	1.01173
	4594	Low confidence	Squared	43959.6	44757.2	1.01814
aminoadipate-semialdehyde synthase; lysine-ketoglutarate reductase /saccharopine dehydrogenase; lysine-2-oxoglutarate reductase; aminoadipic semialdehyde synthase. [refseq;acc:nm_005763]	379	High confidence		40732.2	33010.8	1.23391
	818		Measured	7543.28	6807.78	1.10804
	1319		Rooted	70.1972	67.3443	1.04236
	1863	Low confidence	Measured	8345.43	8081.38	1.03267
	2064	High confidence	Ranked	205.939	207.655	1.00833
	2651	Low confidence	Rooted	74.5089	72.1132	1.03322
	3212		Ranked	199.028	202.212	1.016
	4276		Squared	45390.2	46510.6	1.02468
aminomethyltransferase, mitochondrial precursor (ec 2.1.2.10) (glycine cleavage system t protein) (gcvt). [swissprot;acc:p48728]	1237		Measured	8613.43	8314.67	1.03593
	1317	High confidence	Squared	28816.9	25544.9	1.12809
	1545		Measured	6380.28	5945.96	1.07304
	1877		Rooted	65.5763	63.6973	1.0295
	2544		Ranked	212.262	212.67	1.00192
	2841	Low confidence	Rooted	76.6619	74.2363	1.03267
	2903		Ranked	192.845	196.135	1.01706
	4813		Squared	45391.7	45843.7	1.00996
ammecr1 protein. [refseq;acc:nm_015365]	1062	High confidence	Measured	5913.4	5412.23	1.0926
	1155		Rooted	62.8125	59.9298	1.0481
	1229	Low confidence	Measured	8924.44	8614.27	1.03601
	1577	High confidence	Ranked	218.982	222.585	1.01645
	1675		Squared	26223.8	23713.7	1.10585
	2922	Low confidence	Ranked	190.73	193.976	1.01702
	2953		Rooted	77.9118	75.4744	1.03229
	4999		Squared	49046.2	49004.6	1.00085
amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]	34	High confidence		25146.6	9924.76	2.53372
	52		Ranked	105	133	1.26667
	70		Measured	10307.5	6475.5	1.59177
	116		Rooted	101.526	80.4705	1.26165
	560	Low confidence	Measured	8350.82	7980.85	1.04636
	586		Rooted	75.1214	71.9616	1.04391
	799		Ranked	196.11	201.294	1.02643
	4787		Squared	44575.6	45089.2	1.01152
amphiphysin. [swissprot;acc:p49418]	840			44304.4	46542.4	1.05051
	2389		Ranked	198.416	202.089	1.01851
	2559		Rooted	74.4539	72.0438	1.03345
	3426		Measured	8276.52	8063.62	1.0264
amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410]	69		Rooted	67.1136	60.7884	1.10405
	79		Ranked	208.803	229.144	1.09742
	87	High confidence	Rooted	54.9687	42.2825	1.30003
	97		Measured	3897.1	2820.51	1.3817
	139		Ranked	225.68	271.752	1.20415
	170	Low confidence	Measured	6633.65	6131.26	1.08194
	892		Squared	32745.9	34361.2	1.04933
	2112	High confidence		12711	11682.9	1.088
amyloid beta a4 protein precursor (app) (abpp) (alzheimer's disease amyloid protein) (cerebral vascular amyloid peptide) (cvap) (protease nexin-ii) (pn-ii) (appi) (prea4) [contains: soluble app-alpha (s-app- alpha); soluble app-beta (s-app-beta); c99; beta-amyloid protein 42 (beta-app42); beta-amyloid protein 40 (beta-app40); c83; p3(42); p3(40); gamma-ctf(59) (gamma-secretase c-terminal fragment 59) (amyloid intracellular domain 59) (aid(59)); gamma-ctf(57) (gamma- secretase c-terminal fragment 57) (amyloid intracellular domain 57) (aid(57)); gamma-ctf(50) (gamma-secretase c-terminal fragment 50) (amyloid intracellular domain 50) (aid(50)); c31]. [swissprot;acc:p05067]	508	Low confidence	Ranked	198.715	205.157	1.03242

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.