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

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Showing element 101 to 150 of 33156 in total

Filtered  : 1
Network Comparison Type  : Divided

description	Rank	green	Value Type	Interaction Map	red	network_comparison
14.5 kda translational inhibitor protein (p14.5) (uk114 antigen homolog). [swissprot;acc:p52758]	1600	6788.96	Measured	High confidence	6336.22	1.07145
	2036	68.7832	Rooted		66.966	1.02714
	2366	202.529	Ranked		203.353	1.00407
	4150	44213.2	Squared	Low confidence	45383.4	1.02647
15 kda selenoprotein precursor. [swissprot;acc:o60613]	914	34456.5		High confidence	29772.1	1.15734
	1043	6933.36	Measured		6344.41	1.09283
	1334	67.2624	Rooted		64.5959	1.04128
	1948	212.432	Ranked		214.522	1.00984
	2675	43157.8	Squared	Low confidence	44774.4	1.03746
	3577	8083.96	Measured		7881.96	1.02563
	3869	73.3413	Rooted		71.3287	1.02822
	4465	201.104	Ranked		202.928	1.00907
15-hydroxyprostaglandin dehydrogenase [nad(+)] (ec 1.1.1.141) (pgdh). [swissprot;acc:p15428]	2067	8425.81	Measured		8165.8	1.03184
	2855	0.00001		High confidence	0.00001	1
			Ranked
			Squared
			Rooted
	3576	75.5218		Low confidence	73.3363	1.0298
	4126	195.778	Ranked		197.858	1.01062
	4553	44651.1	Squared		45519.8	1.01946
16.7kd protein. [refseq;acc:nm_016139]	788	45775.4			48142.9	1.05172
	3267	195.864	Ranked		198.949	1.01575
	3651	75.5801	Rooted		73.4106	1.02955
	4005	8483.17	Measured		8297.71	1.02235
17 beta-hydroxysteroid dehydrogenase. [sptrembl;acc:q13034]	1051	217.998	Ranked	High confidence	211.449	1.03097
		8498.04	Measured	Low confidence	8189.31	1.0377
	1381	75.6999	Rooted		72.9975	1.03702
	1803	195.655	Ranked		199.592	1.02012
	2377	27574.1	Squared	High confidence	25809.5	1.06837
	2521	6113.96	Measured		5964.17	1.02511
	2642	63.5847	Rooted		63.9773	1.00617
	4655	45738.2	Squared	Low confidence	46495	1.01655
17-beta-hydroxysteroid dehydrogenase type vii-like. [refseq;acc:nm_182829]	631	8689.28	Measured		8316.12	1.04487
	1116	76.9933	Rooted		74.1433	1.03844
	2142	192.884	Ranked		196.577	1.01915
	4933	45903.5	Squared		46142.7	1.00521
2,4-dienoyl coa reductase 2, peroxisomal; peroxisomal 2,4-dienoyl-coa reductase. [refseq;acc:nm_020664]	447	45146.7			48116.9	1.06579
	3846	198.422	Ranked		201.014	1.01306
	4018	74.6723	Rooted		72.7042	1.02707
	4609	8354	Measured		8218.07	1.01654
2-hydroxyacylsphingosine 1-beta-galactosyltransferase precursor (ec 2.4.1.45) (udp-galactose-ceramide galactosyltransferase) (ceramide udp-galactosyltransferase) (cerebroside synthase). [swissprot;acc:q16880]	1636	40720.1	Squared		42455.4	1.04262
	2443	7708.55	Measured		7480.51	1.03048
	3647	71.2917	Rooted		69.2456	1.02955
	4455	205.097	Ranked		207	1.00928
2-hydroxyphytanoyl-coa lyase (ec 4.1.-.-) (2-hpcl) (hspc279). [swissprot;acc:q9uj83]	930	72.6721	Rooted		69.8925	1.03977
	941	201.99	Ranked		207.026	1.02493
	1393	6192.72	Measured	High confidence	5743.36	1.07824
	1463	62.6331	Rooted		60.3015	1.03867
	1493	42254.4	Squared	Low confidence	44097.2	1.04361
	1593	32473.8		High confidence	29261.2	1.10979

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.