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

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Showing element 1501 to 1550 of 77072 in total

Filtered  : 0

description	Value Type	Rank	Network Comparison Type	green	network_comparison	Interaction Map	red
bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340]	Ranked	237	Divided	9067	1.10114	High confidence	9984
		262	Subtracted		917
		323		11151	832	Low confidence	11983
		436	Divided		1.07461
	Squared	141		26.5621	1.76721	High confidence	15.0305
		394	Subtracted		11.5316
		719	Divided	793.252	1.0273	Low confidence	772.175
		724	Subtracted		21.077
	Rooted	115	Divided	17.542	1.25054		14.0275
		174		18.303	1.15298	High confidence	15.8745
		232	Subtracted		2.4285
		235		17.542	3.5145	Low confidence	14.0275
block 23. [sptrembl;acc:q8nhw5]	Measured	26		5187.87	626.74		4561.13
		153		2159.55	216.23	High confidence	1943.32
		293	Divided		1.11127
		343		5187.87	1.13741	Low confidence	4561.13
	Ranked	117	Subtracted	13334.8	1865.5	High confidence	11469.3
		149	Divided		1.16265
		669		10515.3	1.02223	Low confidence	10749.1
		672	Subtracted		233.8
	Squared	14		49224.6	11090.7		38133.9
		89		16084.7	1529	High confidence	14555.7
		213	Divided	49224.6	1.29084	Low confidence	38133.9
		380		16084.7	1.10504	High confidence	14555.7
	Rooted	388	Subtracted	36.6995	1.841	Low confidence	34.8585
		422		22.0536	0.5793	High confidence	22.6329
		437	Divided		1.02627
		509		36.6995	1.05281	Low confidence	34.8585
blocked early in transport 1 homolog (s. cerevisiae) like; golgi snare 15 kda protein. [refseq;acc:nm_016526]	Measured	224	Subtracted	28156.5	255.5		28412
		777	Divided		1.00907
	Ranked	39		8270.5	1.36509		11290
		66	Subtracted		3019.5
	Squared	26		374712	7414		382126
		744	Divided		1.01979
	Rooted	304	Subtracted	121.885	2.696		119.189
		681	Divided		1.02262
blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577]	Measured	136		154.324	1.30138		200.834
		138		154.279	1.30127		200.759
		184		306.727	1.22281	High confidence	375.07
		185		306.933			375.322
		325	Subtracted		68.389
		327		306.727	68.343		375.07
		614		154.324	46.51	Low confidence	200.834
		616		154.279	46.48		200.759
	Ranked	163		17176.5	1517.4		15659.1
		165		17178.7	1515.9		15662.8
		349	Divided	17176.5	1.0969		15659.1
		351		17178.7	1.09678		15662.8
		363	Subtracted	17180.3	499.6	High confidence	16680.7
		365		17183	499		16684

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.