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

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green	network_comparison	Value Type	Rank	Interaction Map	description	red	Network Comparison Type
5.80678	4.04087	Rooted	199	Low confidence	melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]	9.84765	Subtracted
			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	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]		Divided
	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]		Subtracted
5.86733	1.41064	Squared	206	High confidence	small nuclear ribonucleoprotein associated proteins b and b' (snrnp-b) (sm protein b/b') (sm-b/sm-b') (smb/smb'). [swissprot;acc:p14678]	8.27667	Divided
5.86733	2.40934	Squared	434			8.27667	Subtracted
5.87091	1.77599	Rooted	41		suppressor of actin 1. [refseq;acc:nm_014016]	3.30572	Divided
5.87091	2.56519		218		suppressor of actin 1. [refseq;acc:nm_014016]	3.30572	Subtracted
5.90479	1.18231		351		proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931]	4.72248	Subtracted
5.90479	1.25036		119			4.72248	Divided
5.90864	5.69562	Squared	408		ptd016 protein. [refseq;acc:nm_016125]	0.213018	Subtracted
	5.69562		767	Low confidence			Subtracted
	27.7377		17	Low confidence			Divided
	27.7377		28	High confidence
5.9911	1.90678		114	Low confidence	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]	11.4237
5.9911	5.4326		768	Low confidence		11.4237	Subtracted
6.06104	1.27732	Rooted	110	High confidence	protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236]	7.7419	Divided
6.06104	1.68086		299	High confidence		7.7419	Subtracted
6.08276	1.33558		87	Low confidence	arf gtpase-activating protein. [refseq;acc:nm_133446]	8.12404	Divided
	1.33558		88		up-regulated in liver cancer 1; similar to development- and differentiation-enhancing factor 2. [refseq;acc:nm_017707]		Divided
	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]		Subtracted
6.15501	3.44563	Squared	62	High confidence	elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [swissprot;acc:p04720]	21.2079	Divided
6.15501	15.0529	Squared	386			21.2079	Subtracted
6.23127	1.45391	Rooted	59		metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832]	4.28588	Divided
	1.45391		62	Low confidence			Divided
	1.94539		281	High confidence			Subtracted
	1.94539		375	Low confidence
6.30196	0.05248		486	High confidence	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]	6.24948
6.30196	1.0084		478	High confidence		6.24948	Divided
6.32456	0.23288		776	Low confidence	probable mitochondrial import receptor subunit tom7 homolog (translocase of outer membrane 7 kda subunit homolog) (protein ad- 014). [swissprot;acc:q9p0u1]	6.55744	Subtracted
6.32456	1.03682		589			6.55744	Divided
6.488	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]	8.14325	Divided
6.488	1.65525		436			8.14325	Subtracted
6.50325	20.0687	Measured	14	High confidence	cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]	130.512	Divided
6.50325	124.009	Measured	258			130.512	Subtracted
6.55744	0.98968	Rooted	378		methyltransferase like 2. [refseq;acc:nm_018396]	5.56776	Subtracted
6.55744	1.17775	Rooted	145		methyltransferase like 2. [refseq;acc:nm_018396]	5.56776	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/