Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.

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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 [...,...].

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

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Showing element 501 to 550 of 77072 in total

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green	Value Type	Interaction Map	Rank	red	description	network_comparison	Network Comparison Type
5.39669	Squared	High confidence	42	33.64	nanos (fragment). [sptrembl;acc:q8wy41]	6.23345	Divided
			52	1.22698	selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611]	4.39835	Divided
			358	33.64	nanos (fragment). [sptrembl;acc:q8wy41]	28.2433	Subtracted
			420	1.22698	selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611]	4.16971	Subtracted
		Low confidence	56			4.39835	Divided
		Low confidence	774			4.16971	Subtracted
5.42219		High confidence	91	12.5892	lats homolog 1. [refseq;acc:nm_004690]	2.32179	Divided
			92		sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5]	2.32179	Divided
			400		lats homolog 1. [refseq;acc:nm_004690]	7.16701	Subtracted
			401		sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5]	7.16701	Subtracted
		Low confidence	90		lats homolog 1. [refseq;acc:nm_004690]	2.32179	Divided
			91		sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5]	2.32179	Divided
			761		lats homolog 1. [refseq;acc:nm_004690]	7.16701	Subtracted
			762		sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5]	7.16701	Subtracted
5.56738	Measured	High confidence	11	199.549	serpin b12. [swissprot;acc:q96p63]	35.8425	Divided
		High confidence	168			193.982	Subtracted
		Low confidence	10			35.8425	Divided
			280			193.982	Subtracted
5.56776	Rooted		544	5.83095	adapter-related protein complex 2 alpha 1 subunit (alpha-adaptin a) (adaptor protein complex ap-2 alpha-1 subunit) (clathrin assembly protein complex 2 alpha-a large chain) (100 kda coated vesicle protein a) (plasma membrane adaptor ha2/ap2 adaptin alpha a subunit). [swissprot;acc:o95782]	1.04727	Divided
5.56776	Rooted		768	5.83095		0.26319	Subtracted
5.58446	Squared		61	23.0581	laminin beta-1 chain precursor (laminin b1 chain). [swissprot;acc:p07942]	4.12898	Divided
5.58446	Squared		732	23.0581		17.4736	Subtracted
5.66499	Rooted	High confidence	43	9.92134	40s ribosomal protein s26. [swissprot;acc:p02383]	1.75134	Divided
5.66499	Rooted		115	9.92134	40s ribosomal protein s26. [swissprot;acc:p02383]	4.25635	Subtracted
5.71669	Measured		12	199.249	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	34.8539	Divided
			169			193.532	Subtracted
		Low confidence	11			34.8539	Divided
		Low confidence	281			193.532	Subtracted
5.76	Squared	High confidence	21	0.0236686	succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [swissprot;acc:o14521]	243.36	Divided
5.76		High confidence	407	0.0236686		5.73633	Subtracted
5.80317		Low confidence	15	0.0279126	fk506-binding protein 6 (ec 5.2.1.8) (peptidyl-prolyl cis-trans isomerase) (ppiase) (rotamase) (36 kda fk506 binding protein) (fkbp- 36) (immunophilin fkbp36). [swissprot;acc:o75344]	207.905	Divided
5.80317			766	0.0279126		5.77526	Subtracted
5.80678	Rooted		32	9.84765	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	1.69589	Divided
			33		melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]
			34		melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]
			35		melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]
			36		hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]
			37		melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]
			39		melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]
			40		melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]
			41		melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]
			42		melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]
			43		melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]
			44		melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]
			45		melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]
			47		melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]
			48		melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1]
			196		melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	4.04087	Subtracted
			197		melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]
			198		melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]

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.

- http://analysis.yellowcouch.org/