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

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green	Value Type	Network Comparison Type	red	network_comparison	Interaction Map	Rank	description
5.80678	Rooted	Subtracted	9.84765	4.04087	Low confidence	199	melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]
						200	hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]
						201	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]
						202	melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]
						203	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]
						204	melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]
						205	melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]
						206	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]
						207	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]
						208	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]
						209	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]
						210	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]
5.80679		Divided		1.69589		38	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]
		Divided		1.69589		46	melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]
		Subtracted		4.04086		211	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]
		Subtracted		4.04086		212	melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]
5.86733	Squared	Divided	8.27667	1.41064	High confidence	206	small nuclear ribonucleoprotein associated proteins b and b' (snrnp-b) (sm protein b/b') (sm-b/sm-b') (smb/smb'). [swissprot;acc:p14678]
5.86733	Squared	Subtracted	8.27667	2.40934		434
5.87091	Rooted	Divided	3.30572	1.77599		41	suppressor of actin 1. [refseq;acc:nm_014016]
5.87091		Subtracted	3.30572	2.56519		218	suppressor of actin 1. [refseq;acc:nm_014016]
5.90479		Divided	4.72248	1.25036		119	proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931]
5.90479		Subtracted	4.72248	1.18231		351
5.90864	Squared	Divided	0.213018	27.7377		28	ptd016 protein. [refseq;acc:nm_016125]
		Divided		27.7377	Low confidence	17
		Subtracted		5.69562	High confidence	408
		Subtracted		5.69562	Low confidence	767
5.9911		Divided	11.4237	1.90678		114	protein tyrosine phosphatase type iva, member 2 isoform 1; protein tyrosine phosphatase iva2; protein tyrosine phosphatase iva; phosphatase of regenerating liver 2. [refseq;acc:nm_003479]
5.9911		Subtracted	11.4237	5.4326		768
6.06104	Rooted	Divided	7.7419	1.27732	High confidence	110	protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236]
6.06104		Subtracted	7.7419	1.68086	High confidence	299
6.08276		Divided	8.12404	1.33558	Low confidence	87	arf gtpase-activating protein. [refseq;acc:nm_133446]
		Divided		1.33558		88	up-regulated in liver cancer 1; similar to development- and differentiation-enhancing factor 2. [refseq;acc:nm_017707]
		Subtracted		2.04128		365	arf gtpase-activating protein. [refseq;acc:nm_133446]
		Subtracted		2.04128		366	up-regulated in liver cancer 1; similar to development- and differentiation-enhancing factor 2. [refseq;acc:nm_017707]
6.15501	Squared	Divided	21.2079	3.44563	High confidence	62	elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [swissprot;acc:p04720]
6.15501	Squared	Subtracted	21.2079	15.0529		386
6.23127	Rooted	Divided	4.28588	1.45391		59	metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832]
		Divided		1.45391	Low confidence	62
		Subtracted		1.94539	High confidence	281
		Subtracted		1.94539	Low confidence	375
6.30196		Divided	6.24948	1.0084	High confidence	478	adapter-related protein complex 1 sigma 1b subunit (sigma-adaptin 1b) (adaptor protein complex ap-1 sigma-1b subunit) (golgi adaptor ha1/ap1 adaptin sigma-1b subunit) (clathrin assembly protein complex 1 sigma- 1b small chain) (sigma 1b subunit of ap-1 clathrin) (dc22). [swissprot;acc:p56377]
6.30196		Subtracted	6.24948	0.05248	High confidence	486
6.32456		Divided	6.55744	1.03682	Low confidence	589	probable mitochondrial import receptor subunit tom7 homolog (translocase of outer membrane 7 kda subunit homolog) (protein ad- 014). [swissprot;acc:q9p0u1]
6.32456		Subtracted	6.55744	0.23288		776
6.488		Divided	8.14325	1.25512		112	sarcoplasmic/endoplasmic reticulum calcium atpase 1 (ec 3.6.3.8) (calcium pump 1) (serca1) (sr ca(2+)-atpase 1) (calcium-transporting atpase sarcoplasmic reticulum type, fast twitch skeletal muscle isoform) (endoplasmic reticulum class 1/2 ca(2+) atpase). [swissprot;acc:o14983]
6.488		Subtracted	8.14325	1.65525		436
6.50325	Measured	Divided	130.512	20.0687	High confidence	14	cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]
6.50325	Measured	Subtracted	130.512	124.009		258
6.55744	Rooted	Divided	0.00001	655744		11	sedlin. [swissprot;acc:o14582]
6.55744	Rooted	Divided	0.00001	655744		12	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]

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/