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	green	Value Type	network_comparison	red	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	green	Value Type	network_comparison	red
aminoacylase-1 (ec 3.5.1.14) (n-acyl-l-amino-acid amidohydrolase) (acy-1). [swissprot;acc:q03154]	724	Low confidence	196.371	Ranked	1.02747	201.765
	1420	High confidence	208.229		1.02084	203.979
	2349		8001.45	Measured	1.04406	8353.97
	2479		71.2783	Rooted	1.01173	72.1147
	4594	Low confidence	43959.6	Squared	1.01814	44757.2
aminoadipate-semialdehyde synthase; lysine-ketoglutarate reductase /saccharopine dehydrogenase; lysine-2-oxoglutarate reductase; aminoadipic semialdehyde synthase. [refseq;acc:nm_005763]	379	High confidence	40732.2		1.23391	33010.8
	818		7543.28	Measured	1.10804	6807.78
	1319		70.1972	Rooted	1.04236	67.3443
	1863	Low confidence	8345.43	Measured	1.03267	8081.38
	2064	High confidence	205.939	Ranked	1.00833	207.655
	2651	Low confidence	74.5089	Rooted	1.03322	72.1132
	3212		199.028	Ranked	1.016	202.212
	4276		45390.2	Squared	1.02468	46510.6
aminomethyltransferase, mitochondrial precursor (ec 2.1.2.10) (glycine cleavage system t protein) (gcvt). [swissprot;acc:p48728]	1237		8613.43	Measured	1.03593	8314.67
	1317	High confidence	28816.9	Squared	1.12809	25544.9
	1545		6380.28	Measured	1.07304	5945.96
	1877		65.5763	Rooted	1.0295	63.6973
	2544		212.262	Ranked	1.00192	212.67
	2841	Low confidence	76.6619	Rooted	1.03267	74.2363
	2903		192.845	Ranked	1.01706	196.135
	4813		45391.7	Squared	1.00996	45843.7
ammecr1 protein. [refseq;acc:nm_015365]	1062	High confidence	5913.4	Measured	1.0926	5412.23
	1155		62.8125	Rooted	1.0481	59.9298
	1229	Low confidence	8924.44	Measured	1.03601	8614.27
	1577	High confidence	218.982	Ranked	1.01645	222.585
	1675		26223.8	Squared	1.10585	23713.7
	2922	Low confidence	190.73	Ranked	1.01702	193.976
	2953		77.9118	Rooted	1.03229	75.4744
	4999		49046.2	Squared	1.00085	49004.6
amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]	34	High confidence	25146.6		2.53372	9924.76
	52		105	Ranked	1.26667	133
	70		10307.5	Measured	1.59177	6475.5
	116		101.526	Rooted	1.26165	80.4705
	560	Low confidence	8350.82	Measured	1.04636	7980.85
	586		75.1214	Rooted	1.04391	71.9616
	799		196.11	Ranked	1.02643	201.294
	4787		44575.6	Squared	1.01152	45089.2
amphiphysin. [swissprot;acc:p49418]	840		44304.4		1.05051	46542.4
	2389		198.416	Ranked	1.01851	202.089
	2559		74.4539	Rooted	1.03345	72.0438
	3426		8276.52	Measured	1.0264	8063.62
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		67.1136	Rooted	1.10405	60.7884
	79		208.803	Ranked	1.09742	229.144
	87	High confidence	54.9687	Rooted	1.30003	42.2825
	97		3897.1	Measured	1.3817	2820.51
	139		225.68	Ranked	1.20415	271.752
	170	Low confidence	6633.65	Measured	1.08194	6131.26
	892		32745.9	Squared	1.04933	34361.2
	2112	High confidence	12711		1.088	11682.9
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	198.715	Ranked	1.03242	205.157

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.