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	network_comparison	green	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	network_comparison	green	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	1.10114	9067	High confidence	9984
		262	Subtracted	917
		323		832	11151	Low confidence	11983
		436	Divided	1.07461
	Squared	141		1.76721	26.5621	High confidence	15.0305
		394	Subtracted	11.5316
		719	Divided	1.0273	793.252	Low confidence	772.175
		724	Subtracted	21.077
	Rooted	115	Divided	1.25054	17.542		14.0275
		174		1.15298	18.303	High confidence	15.8745
		232	Subtracted	2.4285
		235		3.5145	17.542	Low confidence	14.0275
block 23. [sptrembl;acc:q8nhw5]	Measured	26		626.74	5187.87		4561.13
		153		216.23	2159.55	High confidence	1943.32
		293	Divided	1.11127
		343		1.13741	5187.87	Low confidence	4561.13
	Ranked	117	Subtracted	1865.5	13334.8	High confidence	11469.3
		149	Divided	1.16265
		669		1.02223	10515.3	Low confidence	10749.1
		672	Subtracted	233.8
	Squared	14		11090.7	49224.6		38133.9
		89		1529	16084.7	High confidence	14555.7
		213	Divided	1.29084	49224.6	Low confidence	38133.9
		380		1.10504	16084.7	High confidence	14555.7
	Rooted	388	Subtracted	1.841	36.6995	Low confidence	34.8585
		422		0.5793	22.0536	High confidence	22.6329
		437	Divided	1.02627
		509		1.05281	36.6995	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	255.5	28156.5		28412
		777	Divided	1.00907
	Ranked	39		1.36509	8270.5		11290
		66	Subtracted	3019.5
	Squared	26		7414	374712		382126
		744	Divided	1.01979
	Rooted	304	Subtracted	2.696	121.885		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		1.30138	154.324		200.834
		138		1.30127	154.279		200.759
		184		1.22281	306.727	High confidence	375.07
		185			306.933		375.322
		325	Subtracted	68.389
		327		68.343	306.727		375.07
		614		46.51	154.324	Low confidence	200.834
		616		46.48	154.279		200.759
	Ranked	163		1517.4	17176.5		15659.1
		165		1515.9	17178.7		15662.8
		349	Divided	1.0969	17176.5		15659.1
		351		1.09678	17178.7		15662.8
		363	Subtracted	499.6	17180.3	High confidence	16680.7
		365		499	17183		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.