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 Network Comparison Type red Gene Interaction Map Rank network_comparison description

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green	Value Type	Network Comparison Type	red	Interaction Map	Rank	network_comparison	description
5.80678	Rooted	Subtracted	9.84765	Low confidence	199	4.04087	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			38	1.69589	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]
		Divided			46	1.69589	melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]
		Subtracted			211	4.04086	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]
		Subtracted			212	4.04086	melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]
5.86733	Squared	Divided	8.27667	High confidence	206	1.41064	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		434	2.40934
5.87091	Rooted	Divided	3.30572		41	1.77599	suppressor of actin 1. [refseq;acc:nm_014016]
5.87091		Subtracted	3.30572		218	2.56519	suppressor of actin 1. [refseq;acc:nm_014016]
5.90479		Divided	4.72248		119	1.25036	proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931]
5.90479		Subtracted	4.72248		351	1.18231
5.90864	Squared	Divided	0.213018		28	27.7377	ptd016 protein. [refseq;acc:nm_016125]
		Divided		Low confidence	17	27.7377
		Subtracted		High confidence	408	5.69562
		Subtracted		Low confidence	767	5.69562
5.9911		Divided	11.4237		114	1.90678	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		768	5.4326
6.06104	Rooted	Divided	7.7419	High confidence	110	1.27732	protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236]
6.06104		Subtracted	7.7419	High confidence	299	1.68086
6.08276		Divided	8.12404	Low confidence	87	1.33558	arf gtpase-activating protein. [refseq;acc:nm_133446]
		Divided			88	1.33558	up-regulated in liver cancer 1; similar to development- and differentiation-enhancing factor 2. [refseq;acc:nm_017707]
		Subtracted			365	2.04128	arf gtpase-activating protein. [refseq;acc:nm_133446]
		Subtracted			366	2.04128	up-regulated in liver cancer 1; similar to development- and differentiation-enhancing factor 2. [refseq;acc:nm_017707]
6.15501	Squared	Divided	21.2079	High confidence	62	3.44563	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		386	15.0529
6.23127	Rooted	Divided	4.28588		59	1.45391	metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832]
		Divided		Low confidence	62	1.45391
		Subtracted		High confidence	281	1.94539
		Subtracted		Low confidence	375	1.94539
6.30196		Divided	6.24948	High confidence	478	1.0084	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	High confidence	486	0.05248
6.32456		Divided	6.55744	Low confidence	589	1.03682	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		776	0.23288
6.488		Divided	8.14325		112	1.25512	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		436	1.65525
6.50325	Measured	Divided	130.512	High confidence	14	20.0687	cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]
6.50325	Measured	Subtracted	130.512		258	124.009
6.55744	Rooted	Divided	0.00001		11	655744	sedlin. [swissprot;acc:o14582]
6.55744	Rooted	Divided	0.00001		12	655744	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/