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

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

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green	network_comparison	Value Type	red	Network Comparison Type	Interaction Map	Rank	description
5.39669	4.16971	Squared	1.22698	Subtracted	High confidence	420	selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611]
	4.16971			Subtracted	Low confidence	774
	4.39835			Divided	High confidence	52
	4.39835				Low confidence	56
	6.23345		33.64		High confidence	42	nanos (fragment). [sptrembl;acc:q8wy41]
	28.2433		33.64	Subtracted		358	nanos (fragment). [sptrembl;acc:q8wy41]
5.42219	2.32179		12.5892	Divided		91	lats homolog 1. [refseq;acc:nm_004690]
						92	sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5]
					Low confidence	90	lats homolog 1. [refseq;acc:nm_004690]
					Low confidence	91	sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5]
	7.16701			Subtracted	High confidence	400	lats homolog 1. [refseq;acc:nm_004690]
					High confidence	401	sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5]
					Low confidence	761	lats homolog 1. [refseq;acc:nm_004690]
					Low confidence	762	sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5]
5.56738	35.8425	Measured	199.549	Divided	High confidence	11	serpin b12. [swissprot;acc:q96p63]
	35.8425			Divided	Low confidence	10
	193.982			Subtracted	High confidence	168
	193.982				Low confidence	280
5.56776	0.26319	Rooted	5.83095			768	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]
5.56776	1.04727	Rooted	5.83095	Divided		544
5.58446	4.12898	Squared	23.0581	Divided		61	laminin beta-1 chain precursor (laminin b1 chain). [swissprot;acc:p07942]
5.58446	17.4736	Squared	23.0581	Subtracted		732
5.66499	1.75134	Rooted	9.92134	Divided	High confidence	43	40s ribosomal protein s26. [swissprot;acc:p02383]
5.66499	4.25635	Rooted	9.92134	Subtracted		115	40s ribosomal protein s26. [swissprot;acc:p02383]
5.71669	34.8539	Measured	199.249	Divided		12	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]
	34.8539			Divided	Low confidence	11
	193.532			Subtracted	High confidence	169
	193.532				Low confidence	281
5.76	5.73633	Squared	0.0236686		High confidence	407	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]
5.76	243.36		0.0236686	Divided	High confidence	21
5.80317	5.77526		0.0279126	Subtracted	Low confidence	766	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]
5.80317	207.905		0.0279126	Divided		15
5.80678	1.69589	Rooted	9.84765			32	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]
						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]
	4.04087			Subtracted		196	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]
						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/