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