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

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green	Rank	Interaction Map	Value Type	network_comparison	description	red	Network Comparison Type
5.80678	199	Low confidence	Rooted	4.04087	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	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]		Divided
	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]		Subtracted
5.86733	206	High confidence	Squared	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]	8.27667	Divided
5.86733	434		Squared	2.40934		8.27667	Subtracted
5.87091	41		Rooted	1.77599	suppressor of actin 1. [refseq;acc:nm_014016]	3.30572	Divided
5.87091	218			2.56519	suppressor of actin 1. [refseq;acc:nm_014016]	3.30572	Subtracted
5.90479	119			1.25036	proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931]	4.72248	Divided
5.90479	351			1.18231		4.72248	Subtracted
5.90864	17	Low confidence	Squared	27.7377	ptd016 protein. [refseq;acc:nm_016125]	0.213018	Divided
	28	High confidence		27.7377			Divided
	408	High confidence		5.69562			Subtracted
	767	Low confidence		5.69562			Subtracted
5.9911	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]	11.4237	Divided
5.9911	768			5.4326		11.4237	Subtracted
6.06104	110	High confidence	Rooted	1.27732	protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236]	7.7419	Divided
6.06104	299	High confidence		1.68086		7.7419	Subtracted
6.08276	87	Low confidence		1.33558	arf gtpase-activating protein. [refseq;acc:nm_133446]	8.12404	Divided
	88			1.33558	up-regulated in liver cancer 1; similar to development- and differentiation-enhancing factor 2. [refseq;acc:nm_017707]		Divided
	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]		Subtracted
6.15501	62	High confidence	Squared	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]	21.2079	Divided
6.15501	386		Squared	15.0529		21.2079	Subtracted
6.23127	59		Rooted	1.45391	metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832]	4.28588	Divided
	62	Low confidence		1.45391			Divided
	281	High confidence		1.94539			Subtracted
	375	Low confidence		1.94539			Subtracted
6.30196	478	High confidence		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]	6.24948	Divided
6.30196	486	High confidence		0.05248		6.24948	Subtracted
6.32456	589	Low confidence		1.03682	probable mitochondrial import receptor subunit tom7 homolog (translocase of outer membrane 7 kda subunit homolog) (protein ad- 014). [swissprot;acc:q9p0u1]	6.55744	Divided
6.32456	776			0.23288		6.55744	Subtracted
6.488	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]	8.14325	Divided
6.488	436			1.65525		8.14325	Subtracted
6.50325	14	High confidence	Measured	20.0687	cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]	130.512	Divided
6.50325	258		Measured	124.009		130.512	Subtracted
6.55744	11		Rooted	655744	sedlin. [swissprot;acc:o14582]	0.00001	Divided
6.55744	12		Rooted	655744	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	0.00001	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/