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

Results: HTML CSV LaTeX

Showing element 501 to 550 of 77072 in total

Filtered

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green	network_comparison	Value Type	Interaction Map	description	Network Comparison Type	Rank	red
5.39669	4.16971	Squared	High confidence	selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611]	Subtracted	420	1.22698
	4.16971		Low confidence		Subtracted	774
	4.39835		High confidence		Divided	52
	4.39835		Low confidence			56
	6.23345		High confidence	nanos (fragment). [sptrembl;acc:q8wy41]		42	33.64
	28.2433			nanos (fragment). [sptrembl;acc:q8wy41]	Subtracted	358	33.64
5.42219	2.32179			lats homolog 1. [refseq;acc:nm_004690]	Divided	91	12.5892
				sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5]		92
			Low confidence	lats homolog 1. [refseq;acc:nm_004690]		90
			Low confidence	sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5]		91
	7.16701		High confidence	lats homolog 1. [refseq;acc:nm_004690]	Subtracted	400
			High confidence	sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5]		401
			Low confidence	lats homolog 1. [refseq;acc:nm_004690]		761
			Low confidence	sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5]		762
5.56738	35.8425	Measured	High confidence	serpin b12. [swissprot;acc:q96p63]	Divided	11	199.549
	35.8425		Low confidence		Divided	10
	193.982		High confidence		Subtracted	168
	193.982		Low confidence			280
5.56776	0.26319	Rooted		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]		768	5.83095
5.56776	1.04727	Rooted			Divided	544	5.83095
5.58446	4.12898	Squared		laminin beta-1 chain precursor (laminin b1 chain). [swissprot;acc:p07942]	Divided	61	23.0581
5.58446	17.4736	Squared			Subtracted	732	23.0581
5.66499	1.75134	Rooted	High confidence	40s ribosomal protein s26. [swissprot;acc:p02383]	Divided	43	9.92134
5.66499	4.25635	Rooted		40s ribosomal protein s26. [swissprot;acc:p02383]	Subtracted	115	9.92134
5.71669	34.8539	Measured		hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	Divided	12	199.249
	34.8539		Low confidence		Divided	11
	193.532		High confidence		Subtracted	169
	193.532		Low confidence			281
5.76	5.73633	Squared	High confidence	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]		407	0.0236686
5.76	243.36		High confidence		Divided	21	0.0236686
5.80317	5.77526		Low confidence	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]	Subtracted	766	0.0279126
5.80317	207.905				Divided	15	0.0279126
5.80678	1.69589	Rooted		hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]		36	9.84765
				melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]		32
				melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]		45
				melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]		34
				melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]		44
				melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]		35
				melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]		33
				melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]		40
				melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]		37
				melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]		42
				melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]		41
				melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]		47
				melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]		43
				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]		48
				melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]		39
	4.04087			hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]	Subtracted	200
				melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]		196
				melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]		208

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/