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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

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

Results: HTML CSV LaTeX

Showing element 2125 to 2174 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

description	Rank	Hugo	Value Type	Network Comparison Type	red	green	network_comparison
alveolar soft part sarcoma chromosome region, candidate 1; aspl protein; renal cell carcinoma gene on chromosome 17; renal cell carcinoma, papillary, 17 gene; aspscr1/tfe3 fusion gene, included. [refseq;acc:nm_024083]	2829	ASPSCR1	Squared	Divided	0.00001	0.00001	1
				Subtracted	0	0	0
			Rooted	Divided	0.00001	0.00001	1
				Subtracted	0	0	0
amidophosphoribosyltransferase precursor (ec 2.4.2.14) (glutamine phosphoribosylpyrophosphate amidotransferase) (atase) (gpat). [swissprot;acc:q06203]	569	PPAT	Ranked		228.639	242.258	13.619
	637			Divided			1.05957
	1503		Squared		18555.4	20672	1.11407
	1698		Rooted		56.6562	54.8538	1.03286
	1950		Squared	Subtracted	18555.4	20672	2116.6
	1952		Rooted		56.6562	54.8538	1.8024
	2550		Measured	Divided	4725.79	4824.4	1.02087
	2571			Subtracted			98.61
aminoacylase-1 (ec 3.5.1.14) (n-acyl-l-amino-acid amidohydrolase) (acy-1). [swissprot;acc:q03154]	264	ACY1	Squared		53174	44377.4	8796.6
	524			Divided			1.19822
	1420		Ranked		203.979	208.229	1.02084
	1424			Subtracted			4.25
	1950		Measured		8353.97	8001.45	352.52
	2349			Divided			1.04406
	2460		Rooted	Subtracted	72.1147	71.2783	0.8364
	2479			Divided			1.01173
aminoadipate-semialdehyde synthase; lysine-ketoglutarate reductase /saccharopine dehydrogenase; lysine-2-oxoglutarate reductase; aminoadipic semialdehyde synthase. [refseq;acc:nm_005763]	307	AASS	Squared	Subtracted	33010.8	40732.2	7721.4
	379			Divided			1.23391
	620		Measured	Subtracted	6807.78	7543.28	735.5
	818			Divided			1.10804
	1212		Rooted	Subtracted	67.3443	70.1972	2.8529
	1319			Divided			1.04236
	2064		Ranked		207.655	205.939	1.00833
	2067			Subtracted			1.716
aminomethyltransferase, mitochondrial precursor (ec 2.1.2.10) (glycine cleavage system t protein) (gcvt). [swissprot;acc:p48728]	1087	AMT	Squared		25544.9	28816.9	3272
	1317			Divided			1.12809
	1535		Measured	Subtracted	5945.96	6380.28	434.32
	1545			Divided			1.07304
	1862		Rooted	Subtracted	63.6973	65.5763	1.879
	1877			Divided			1.0295
	2537		Ranked	Subtracted	212.67	212.262	0.408
	2544			Divided			1.00192
ammecr1 protein. [refseq;acc:nm_015365]	1062	AMMECR1	Measured		5412.23	5913.4	1.0926
	1155		Rooted		59.9298	62.8125	1.0481
	1183		Measured	Subtracted	5412.23	5913.4	501.17
	1198		Rooted		59.9298	62.8125	2.8827
	1562		Ranked		222.585	218.982	3.603
	1577			Divided			1.01645
	1613		Squared	Subtracted	23713.7	26223.8	2510.1
	1675			Divided			1.10585
amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]	15	AMPD2	Rooted	Subtracted	80.4705	101.526	21.0555
	34		Squared	Divided	9924.76	25146.6	2.53372
	52		Ranked		133	105	1.26667
	64		Measured	Subtracted	6475.5	10307.5	3832
	70			Divided			1.59177
	116		Rooted		80.4705	101.526	1.26165

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.