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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.

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

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Showing element 551 to 600 of 77072 in total

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green	Value Type	network_comparison	Rank	Interaction Map	description	red	Network Comparison Type
5.80678	Rooted	4.04087	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	Squared	1.41064	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	Squared	2.40934	434			8.27667	Subtracted
5.87091	Rooted	1.77599	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	Squared	5.69562	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	Rooted	1.27732	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	Squared	3.44563	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	Squared	15.0529	386			21.2079	Subtracted
6.23127	Rooted	1.45391	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	Measured	20.0687	14	High confidence	cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]	130.512	Divided
6.50325	Measured	124.009	258			130.512	Subtracted
6.55744	Rooted	0.98968	378		methyltransferase like 2. [refseq;acc:nm_018396]	5.56776	Subtracted
6.55744	Rooted	1.17775	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/