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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Rank Gene Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2658 to 2707 of 3228 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	Hugo	description	red	green	network_comparison	
2658	DLG4	presynaptic density protein 95 (psd-95) (discs, large homolog 4) (postsynaptic density-95). [source:swissprot;acc:p78352]	216.933	216.7	1.00108	
2659	DLG3	presynaptic protein sap102 (synapse-associated protein 102) (neuroendocrine-dlg) (ne-dlg) (discs, large homolog 3). [source:swissprot;acc:q92796]	216.933	216.7	1.00108	
2660	DLG1	presynaptic protein sap97 (synapse-associated protein 97) (discs, large homolog 1) (hdlg). [source:swissprot;acc:q12959]	216.937	216.704	1.00108	
2661	FES	proto-oncogene tyrosine-protein kinase fes/fps (ec 2.7.1.112) (c-fes). [source:swissprot;acc:p07332]	204.768	204.549	1.00107	
2662	MOCS2	molybdenum cofactor synthesis protein 2 large subunit (molybdopterin synthase large subunit) (mpt synthase large subunit) (mocs2b) (moco1- b). [source:swissprot;acc:o96007]	204.768	204.549	1.00107	
2663	ANAPC10	anaphase-promoting complex subunit 10; anaphase-promoting complex 10. [source:refseq;acc:nm_014885]	204.768	204.549	1.00107	
2664	RPL29	60s ribosomal protein l29 (cell surface heparin binding protein hip). [source:swissprot;acc:p47914]	204.768	204.549	1.00107	
2665	FER	proto-oncogene tyrosine-protein kinase fer (ec 2.7.1.112) (p94-fer) (c-fer). [source:swissprot;acc:p16591]	204.768	204.549	1.00107	
2666	TXNDC1	thioredoxin domain containing; thioredoxin-related transmembrane protein; thioredoxin domain-containing. [source:refseq;acc:nm_030755]	210.136	209.911	1.00107	
2667	MOCS3	molybdenum cofactor synthesis protein 3 (molybdopterin synthase sulfurylase) (mpt synthase sulfurylase). [source:swissprot;acc:o95396]	204.768	204.549	1.00107	
2668	FUBP3	fuse binding protein 3 (fragment). [source:sptrembl;acc:q92946]	217.176	216.944	1.00107	
2669	GPD1	glycerol-3-phosphate dehydrogenase [nad+], cytoplasmic (ec 1.1.1.8) (gpd-c) (gpdh-c). [source:swissprot;acc:p21695]	214.575	214.354	1.00103	
2670	KRAS	transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [source:swissprot;acc:p01116]	144.391	144.538	1.00102	
2671	GNPNAT1	similar to glucosamine-phosphate n-acetyltransferase (hypothetical protein flj33258). [source:sptrembl;acc:q96ek6]	216.288	216.067	1.00102	
2672	BCAT1	branched-chain amino acid aminotransferase, cytosolic (ec 2.6.1.42) (bcat(c)) (eca39 protein). [source:swissprot;acc:p54687]	210.957	210.741	1.00102	
2673	RAD9A	rad9 homolog; cell cycle checkpoint control protein; rad9 homolog (s. pombe). [source:refseq;acc:nm_004584]	216.372	216.588	1.001	
2674	GLUL	glutamine synthetase (ec 6.3.1.2) (glutamate--ammonia ligase). [source:swissprot;acc:p15104]	203.151	202.948	1.001	
2675	MRPS26	28s ribosomal protein s26, mitochondrial precursor (mrp-s26) (mrp- s13). [source:swissprot;acc:q9byn8]	214.893	215.108	1.001	
2676	ERH	enhancer of rudimentary homolog. [source:swissprot;acc:q14259]	214.893	215.108	1.001	
2677	SHOC2	leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [source:swissprot;acc:q9uq13]	144.412	144.553	1.00098	
2678		ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [source:swissprot;acc:o15211]	144.411	144.552	1.00098	
2679	ANAPC2	anaphase-promoting complex subunit 2; anaphase-promoting complex 2. [source:refseq;acc:nm_013366]	190.142	189.959	1.00096	
2680	HRAS	transforming protein p21/h-ras-1 (c-h-ras). [source:swissprot;acc:p01112]	144.422	144.56	1.00096	
2681	OTUB2	ubiquitin-specific protease otubain 2. [source:refseq;acc:nm_023112]	203.592	203.787	1.00096	
2682		transforming protein n-ras. [source:swissprot;acc:p01111]	144.427	144.564	1.00095	
2683	YBX1	nuclease sensitive element binding protein 1 (y box binding protein-1) (y-box transcription factor) (yb-1) (ccaat-binding transcription factor i subunit a) (cbf-a) (enhancer factor i subunit a) (efi-a) (dna-binding protein b) (dbpb). [source:swissprot;acc:p16991]	208.438	208.635	1.00095	
2684	CSDA	dna-binding protein a (cold shock domain protein a) (single-strand dna binding protein nf-gmb). [source:swissprot;acc:p16989]	208.438	208.635	1.00095	
2685	YBX2	germ cell specific y-box binding protein; contrin. [source:refseq;acc:nm_015982]	208.438	208.635	1.00095	
2686	PSMB7	proteasome subunit beta type 7 precursor (ec 3.4.25.1) (proteasome subunit z) (macropain chain z) (multicatalytic endopeptidase complex chain z). [source:swissprot;acc:q99436]	219.829	219.629	1.00091	
2687	BCAT2	branched-chain amino acid aminotransferase, mitochondrial precursor (ec 2.6.1.42) (bcat(m)) (placental protein 18) (pp18). [source:swissprot;acc:o15382]	210.939	210.755	1.00087	
2688		peroxisomal 3,2-trans-enoyl-coa isomerase (ec 5.3.3.8) (dodecenoyl-coa delta-isomerase) (d3,d2-enoyl-coa isomerase) (dbi-related protein 1) (drs-1) (hepatocellular carcinoma-associated antigen 88). [source:swissprot;acc:o75521]	194.557	194.392	1.00085	
2689	ACLY	atp-citrate synthase (ec 2.3.3.8) (atp-citrate (pro-s-)-lyase) (citrate cleavage enzyme). [source:swissprot;acc:p53396]	213.792	213.619	1.00081	
2690	AQP4	aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [source:swissprot;acc:p55087]	188.191	188.046	1.00077	
2691	AQP2	aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [source:swissprot;acc:p41181]	188.193	188.048	1.00077	
2692	AQP5	aquaporin 5. [source:swissprot;acc:p55064]	188.192	188.048	1.00077	
2693	MIP	lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [source:swissprot;acc:p30301]	188.193	188.049	1.00077	
2694	AQP1	aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [source:swissprot;acc:p29972]	188.223	188.081	1.00075	
2695	SRP54	signal recognition particle 54 kda protein (srp54). [source:swissprot;acc:p13624]	215.545	215.384	1.00075	
2696	ACO1	iron-responsive element binding protein 1 (ire-bp 1) (iron regulatory protein 1) (irp1) (ferritin repressor protein) (aconitate hydratase) (ec 4.2.1.3) (citrate hydro-lyase) (aconitase). [source:swissprot;acc:p21399]	201.652	201.794	1.0007	
2697	ARPC2	arp2/3 complex 34 kda subunit (p34-arc) (actin-related protein 2/3 complex subunit 2). [source:swissprot;acc:o15144]	225.081	225.232	1.00067	
2698	SSR4	translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [source:swissprot;acc:p51571]	188.435	188.31	1.00066	
2699	CLSTN1	calsyntenin-1 precursor. [source:swissprot;acc:o94985]	188.435	188.31	1.00066	
2700		succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [source:swissprot;acc:o14521]	188.435	188.31	1.00066	
2701	DCLK1	serine/threonine-protein kinase dcamkl1 (ec 2.7.1.-) (doublecortin- like and cam kinase-like 1). [source:swissprot;acc:o15075]	216.539	216.682	1.00066	
2702	PTPRB	protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [source:swissprot;acc:p23467]	188.435	188.311	1.00066	
2703	PRSS16	thymus-specific serine protease precursor (ec 3.4.-.-). [source:swissprot;acc:q9nqe7]	188.435	188.311	1.00066	
2704	CCDC47	gk001 protein. [source:refseq;acc:nm_020198]	188.435	188.311	1.00066	
2705	CLSTN2	calsyntenin-2 precursor. [source:swissprot;acc:q9h4d0]	188.457	188.334	1.00065	
2706	CLSTN3	calsyntenin-3 precursor. [source:swissprot;acc:q9bqt9]	188.459	188.336	1.00065	
2707	ACP1	red cell acid phosphatase 1, isozyme f (ec 3.1.3.2) (acp1) (low molecular weight phosphotyrosine protein phosphatase) (ec 3.1.3.48) (adipocyte acid phosphatase, isozyme alpha). [source:swissprot;acc:p24666]	215.096	215.232	1.00063	

Legend:
- Rank is the rank after comparing the two networks
- Hugo is the HGNC identifier if it exists
- 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/