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

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Showing element 551 to 600 of 77072 in total

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green	description	Value Type	network_comparison	red	Interaction Map	Rank	Network Comparison Type
5.80678	melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]	Rooted	1.69589	9.84765	Low confidence	42	Divided
			4.04087			205	Subtracted
	melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]		1.69589			41	Divided
			4.04087			204	Subtracted
	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]		1.69589			47	Divided
			4.04087			209	Subtracted
	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]		1.69589			43	Divided
			4.04087			206	Subtracted
	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]		1.69589			48	Divided
			4.04087			210	Subtracted
	melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]		1.69589			39	Divided
			4.04087			202	Subtracted
5.80679	melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]		1.69589			46	Divided
			4.04086			212	Subtracted
	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]		1.69589			38	Divided
			4.04086			211	Subtracted
5.86733	small nuclear ribonucleoprotein associated proteins b and b' (snrnp-b) (sm protein b/b') (sm-b/sm-b') (smb/smb'). [swissprot;acc:p14678]	Squared	1.41064	8.27667	High confidence	206	Divided
5.86733		Squared	2.40934	8.27667		434	Subtracted
5.87091	suppressor of actin 1. [refseq;acc:nm_014016]	Rooted	1.77599	3.30572		41	Divided
5.87091	suppressor of actin 1. [refseq;acc:nm_014016]		2.56519	3.30572		218	Subtracted
5.90479	proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931]		1.18231	4.72248		351	Subtracted
5.90479			1.25036	4.72248		119	Divided
5.90864	ptd016 protein. [refseq;acc:nm_016125]	Squared	5.69562	0.213018		408	Subtracted
			5.69562		Low confidence	767	Subtracted
			27.7377		High confidence	28	Divided
			27.7377		Low confidence	17
5.9911	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]		1.90678	11.4237		114
5.9911			5.4326	11.4237		768	Subtracted
6.06104	protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236]	Rooted	1.27732	7.7419	High confidence	110	Divided
6.06104			1.68086	7.7419	High confidence	299	Subtracted
6.08276	arf gtpase-activating protein. [refseq;acc:nm_133446]		1.33558	8.12404	Low confidence	87	Divided
	arf gtpase-activating protein. [refseq;acc:nm_133446]		2.04128			365	Subtracted
	up-regulated in liver cancer 1; similar to development- and differentiation-enhancing factor 2. [refseq;acc:nm_017707]		1.33558			88	Divided
			2.04128			366	Subtracted
6.15501	elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [swissprot;acc:p04720]	Squared	3.44563	21.2079	High confidence	62	Divided
6.15501		Squared	15.0529	21.2079		386	Subtracted
6.23127	metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832]	Rooted	1.45391	4.28588		59	Divided
			1.45391		Low confidence	62	Divided
			1.94539		High confidence	281	Subtracted
			1.94539		Low confidence	375
6.30196	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]		0.05248	6.24948	High confidence	486
6.30196			1.0084	6.24948	High confidence	478	Divided
6.32456	probable mitochondrial import receptor subunit tom7 homolog (translocase of outer membrane 7 kda subunit homolog) (protein ad- 014). [swissprot;acc:q9p0u1]		0.23288	6.55744	Low confidence	776	Subtracted
6.32456			1.03682	6.55744		589	Divided
6.488	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]		1.25512	8.14325		112	Divided
6.488			1.65525	8.14325		436	Subtracted
6.50325	cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]	Measured	20.0687	130.512	High confidence	14	Divided
6.50325		Measured	124.009	130.512		258	Subtracted
6.55744	methyltransferase like 2. [refseq;acc:nm_018396]	Rooted	0.98968	5.56776		378	Subtracted
6.55744	methyltransferase like 2. [refseq;acc:nm_018396]	Rooted	1.17775	5.56776		145	Divided

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/