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

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Showing element 6408 to 6457 of 66312 in total

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description	Rank	Network Comparison Type	Value Type	Hugo	Interaction Map	red	green	network_comparison
aspartyl-trna synthetase (ec 6.1.1.12) (aspartate--trna ligase) (asprs). [swissprot;acc:p14868]	2026	Divided	Measured	DARS	High confidence	6766.45	7155.54	1.0575
	2042		Ranked		Low confidence	200.776	196.962	1.01936
	2052	Subtracted						3.814
	2280		Rooted		High confidence	70.2102	71.5141	1.3039
	2327	Divided						1.01857
	2541		Ranked			194.505	194.902	1.00204
	2544	Subtracted						0.397
	3880		Squared		Low confidence	46556.2	45300.7	1255.5
	4046	Divided						1.02771
associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799]	49			STAMBPL1	High confidence	28994.2	17134.8	1.69212
	102	Subtracted	Measured			11068	8508.5	2559.5
	126	Divided	Ranked			94	114	1.21277
	141	Subtracted	Rooted			105.205	92.2415	12.9635
	146	Divided	Measured			11068	8508.5	1.30082
	181		Ranked		Low confidence	196.362	206.979	1.05407
	189	Subtracted						10.617
	211		Squared		High confidence	28994.2	17134.8	11859.4
	213	Divided	Rooted			105.205	92.2415	1.14054
	353	Subtracted	Ranked			94	114	20
	2133	Divided	Squared		Low confidence	38260.9	36807.4	1.03949
	3325	Subtracted						1453.5
	3714	Divided	Measured			7382.5	7204.94	1.02464
	4160	Subtracted						177.56
	4172	Divided	Rooted			71.0543	69.2972	1.02536
	4398	Subtracted						1.7571
associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463]	51	Divided	Squared	STAMBP	High confidence	28994.2	17134.8	1.69212
	104	Subtracted	Measured			11068	8508.5	2559.5
	128	Divided	Ranked			94	114	1.21277
	143	Subtracted	Rooted			105.205	92.2415	12.9635
	148	Divided	Measured			11068	8508.5	1.30082
	186		Ranked		Low confidence	196.381	206.921	1.05367
	196	Subtracted						10.54
	213		Squared		High confidence	28994.2	17134.8	11859.4
	215	Divided	Rooted			105.205	92.2415	1.14054
	355	Subtracted	Ranked			94	114	20
	2146	Divided	Squared		Low confidence	38297.9	36846.9	1.03938
	3339	Subtracted						1451
	3766	Divided	Measured			7386.18	7211.2	1.02427
	4187	Subtracted						174.98
	4200	Divided	Rooted			71.0627	69.3294	1.025
	4431	Subtracted						1.7333
ataxia telangiectasia and rad3 related protein; rad3 related protein; frap-related protein-1; protein kinase atr; seckel syndrome. [refseq;acc:nm_001184]	2104		Measured	ATR		8047.27	8299.86	252.59
	2204	Divided						1.03139
	2366	Subtracted	Rooted			72.1805	74.6322	2.4517
	2372	Divided						1.03397
	2730	Subtracted	Ranked			201.497	198.046	3.451
	2766	Divided						1.01743
	3258	Subtracted	Squared			45749.4	44280.8	1468.6
	3412	Divided						1.03317
ataxin 2 related protein isoform a; ataxin-2 domain protein. [refseq;acc:nm_007245]	602		Measured	ATXN2L	High confidence	4864.66	5514.87	1.13366

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
- Hugo is the HGNC identifier if it exists
- 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.