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

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Showing element 401 to 450 of 77072 in total

Filtered  : 0
Value Type  : Measured

description	Rank	Network Comparison Type	network_comparison	Interaction Map	green	red
bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [swissprot;acc:p34820]	74	Divided	1.71473	High confidence	859.34	501.151
	91	Subtracted	358.189
	357	Divided	1.12788	Low confidence	583.626	517.453
	536	Subtracted	66.173
brain protein 16. [refseq;acc:nm_016458]	124		262.39	High confidence	2418.14	2155.75
	274	Divided	1.12172
	311	Subtracted	165.09	Low confidence	2837.61	3002.7
	512	Divided	1.05818
brca1 associated protein. [refseq;acc:nm_006768]	157		1.25567		1403.03	1117.36
	202	Subtracted	285.67
	502	Divided	1	High confidence	0.00001	0.00001
		Subtracted	0		0	0
bromodomain adjacent to zinc finger domain protein 1a (atp-utilizing chromatin assembly and remodeling factor 1) (hacf1) (atp-dependent chromatin remodelling protein) (williams syndrome transcription factor-related chromatin remodeling factor 180) (wcrf180) (hwalp1) (chrac subunit acf1) (hspc317). [swissprot;acc:q9nrl2]	189	Divided	1.19632	Low confidence	434.871	363.508
	509	Subtracted	71.363
butyrate-induced transcript 1. [refseq;acc:nm_016395]	744		19.87		4703	4683.13
	801	Divided	1.00424
bystin. [swissprot;acc:q13895]	160	Subtracted	204.88	High confidence	3135.76	2930.88
	343	Divided	1.0699
	626	Subtracted	43.55	Low confidence	2357.34	2313.79
	693	Divided	1.01882
c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02]	192	Subtracted	167.74	High confidence	1463.55	1295.81
	261	Divided	1.12945
	330	Subtracted	148.98	Low confidence	1624.78	1475.8
	405	Divided	1.10095
cab2. [refseq;acc:nm_033419]	2		17400000	High confidence	174	0.00001
	76		1.77407	Low confidence	128.776	72.5877
	185	Subtracted	174	High confidence	174	0
	565		56.1883	Low confidence	128.776	72.5877
calcyphosine. [swissprot;acc:q13938]	126	Divided	1.3457	High confidence	635.875	472.524
	194	Subtracted	163.351
	562		56.99	Low confidence	1454.03	1397.04
	584	Divided	1.04079
calponin h2, smooth muscle (neutral calponin). [swissprot;acc:q99439]	114		1.36592		1049.11	768.061
	205	Subtracted	281.049
camp-dependent protein kinase, gamma-catalytic subunit (ec 2.7.1.37) (pka c-gamma). [swissprot;acc:p22612]	255		124.74	High confidence	2633.79	2509.05
	381	Divided	1.04972
	623		1.03208	Low confidence	889.914	862.25
	695	Subtracted	27.664
camp-regulated phosphoprotein 19 (arpp-19) [contains: camp-regulated phosphoprotein 16 (arpp-16)]. [swissprot;acc:p56211]	18	Divided	5.21053		19	99
	483	Subtracted	80
candidate tumor suppressor protein. [refseq;acc:nm_020381]	27		589.67		2821.67	2232
	153	Divided	1.26419
carbohydrate (n-acetylglucosamine 6-o) sulfotransferase 6; macular dystrophy, corneal, 1; carbohydate sulfotransferase 6; corneal n-acetylglucosamine 6-sulfotransferase. [refseq;acc:nm_021615]	22		3700000		0.00001	37
	648	Subtracted	37		0
carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267]	23	Divided	3700000		0.00001
	649	Subtracted	37		0
carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870]	23		718.23		5584.69	6302.92
	316	Divided	1.09714	High confidence	576	525
	352		1.12861	Low confidence	5584.69	6302.92
	359	Subtracted	51	High confidence	576	525

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.