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	Value Type	Network Comparison Type	Interaction Map	Filtered	red	green	network_comparison

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Showing element 9536 to 9585 of 9634 in total

Value Type  : Measured
Network Comparison Type  : Divided

description	Rank	Interaction Map	Filtered	red	green	network_comparison
zinc finger protein 8 (zinc finger protein hf.18) (fragment). [swissprot;acc:p17098]	4407	Low confidence	1	9143.33	9323.18	1.01967
zinc finger protein 80 (znfpt17). [swissprot;acc:p51504]	290		0	2355.8	1972.55	1.19429
	4296		1	9143.33	9323.18	1.01967
zinc finger protein 83 (zinc finger protein hpf1). [swissprot;acc:p51522]	235		0	2351.92	1968.97	1.19449
	4385		1	9143.34	9323.19	1.01967
zinc finger protein 84 (zinc finger protein hpf2). [swissprot;acc:p51523]	218		0	2351.3	1968.39	1.19453
	4403		1	9143.35	9323.2	1.01967
zinc finger protein 85 (zinc finger protein hpf4) (htf1). [swissprot;acc:q03923]	208		0	2351.07	1968.18	1.19454
	4394		1	9143.35	9323.2	1.01967
zinc finger protein 92 (zinc finger protein htf12) (fragment). [swissprot;acc:q03936]	221		0	2351.45	1968.53	1.19452
	4357		1	9143.35	9323.19	1.01967
zinc finger protein 93 (zinc finger protein htf34) (fragment). [swissprot;acc:p35789]	204		0	2351.01	1968.12	1.19455
	4409		1	9143.35	9323.2	1.01967
zinc finger protein 93 (zinc finger protein htf34). [refseq;acc:nm_145312]	225		0	2351.51	1968.59	1.19451
	4332		1	9143.35	9323.19	1.01967
zinc finger protein 95 homolog (zfp-95). [swissprot;acc:q9y2l8]	293		0	2356.02	1972.76	1.19428
	4413		1	9143.33	9323.18	1.01967
zinc finger protein 99. [refseq;acc:nm_032164]	2479	High confidence		3568.99	3676.6	1.03015
	4116	Low confidence		7963.3	8132.15	1.0212
zinc finger protein af020591. [refseq;acc:nm_014480]	213		0	2351.15	1968.26	1.19453
	4362		1	9143.35	9323.2	1.01967
zinc finger protein basonuclin. [swissprot;acc:q01954]	3452			11743.8	11443.5	1.02624
zinc finger protein bioref. [swissprot;acc:q9hck0]	4003			8230.1	8414.08	1.02235
zinc finger protein clone 647. [swissprot;acc:p15622]	4308			9143.35	9323.19	1.01967
zinc finger protein gli1 (glioma-associated oncogene) (oncogene gli). [swissprot;acc:p08151]	1184	High confidence		4392.63	4776.19	1.08732
	3481	Low confidence		8069.85	8280.48	1.0261
zinc finger protein gli2 (tax helper protein). [swissprot;acc:p10070]	1189	High confidence		4392.63	4776.19	1.08732
	3483	Low confidence		8070.79	8281.29	1.02608
zinc finger protein gli3. [swissprot;acc:p10071]	1186	High confidence		4392.63	4776.19	1.08732
	3527	Low confidence		8083.75	8292.55	1.02583
zinc finger protein loc163140 (fragment). [sptrembl;acc:q86wm6]	198		0	2350.92	1968.04	1.19455
	4286		1	9143.35	9323.2	1.01967
zinc finger protein mgc21738. [refseq;acc:nm_145044]	257		0	2352.73	1969.72	1.19445
	4263		1	9143.34	9323.19	1.01967
zinc finger protein plzf (promyelocytic leukemia zinc finger protein) (zinc finger protein 145). [swissprot;acc:q05516]	4392			9143.31	9323.18
zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623]	38	High confidence	0	320.012	120.429	2.65727
	521	Low confidence		2077.04	2192.97	1.05582
	1636	High confidence	1	9899.73	9251.16	1.07011
	4756	Low confidence		7693.28	7792.25	1.01286
zinc finger protein t86. [swissprot;acc:o00488]	546	High confidence		4052.77	4612.54	1.13812
	1861	Low confidence		7864.01	8120.92	1.03267
zinc finger protein with interaction domain. [refseq;acc:nm_006626]	3995			8230.09	8414.14	1.02236
zinc finger protein zfd25. [swissprot;acc:q9uii5]	261		0	2352.64	1969.64	1.19445
	4298		1	9143.34	9323.19	1.01967
zinc finger protein zfp-36 (fragment). [swissprot;acc:p16415]	271		0	2353.27	1970.21	1.19443
	4397		1	9143.34	9323.19	1.01967
zinc finger protein zfp. [refseq;acc:nm_018651]	205		0	2350.96	1968.08	1.19454
	4261		1	9143.35	9323.2	1.01967
zinc finger protein zfp31 (fragment). [sptrembl;acc:q92971]	231		0	2351.86	1968.91	1.1945
	4383		1	9143.34	9323.19	1.01967

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.