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 Network Type I Analysis

Type 1 network in which we propagated the absolute log regulation ratio abs(log(r/g)). We used the filtered lowest boundary of the confidence interval for the microarray measurement based and used the high confidence interaction map. Because type-I networks tend to favour highly connected proteins we tested a normalisation scheme in which we would run the network once with real values (the measured column) and once with simulated values where each measured point is set to 1 instead of the actual signal (the expected column). Afterwards we divided the measured value by the expected value. This normalisation scheme works to a certain extend but will lead to a variance that is directly related to the connectivity of each protein. In the end we dropped the use of Type-I networks due to the many technical problems they pose.

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Rank Gene description measured expected final Hugo

Results: HTML CSV LaTeX

Showing element 1952 to 2001 of 3206 in total

Rank	description	measured	expected	final	Hugo	
1952	RIBOSE 5-PHOSPHATE ISOMERASE (EC 5.3.1.6) (PHOSPHORIBOISOMERASE). [Source:SWISSPROT;Acc:P49247]	0.128195	0.554305	0.231271592	RPIA	
1953	60S RIBOSOMAL PROTEIN L14 (CAG-ISL 7). [Source:SWISSPROT;Acc:P50914]	0.0571361	0.247068	0.231256577		
1954	PROTEIN TRANSPORT PROTEIN SEC61 ALPHA SUBUNIT ISOFORM 1 (SEC61 ALPHA- 1). [Source:SWISSPROT;Acc:P38378]	1.32564	5.73234	0.231256346	SEC61A1	
1955	SERINE RACEMASE (EC 5.1.1.-). [Source:SWISSPROT;Acc:Q9GZT4]	0.0573513	0.247999	0.231256174	SRR	
1956	60S RIBOSOMAL PROTEIN L34. [Source:SWISSPROT;Acc:P49207]	0.0382183	0.165264	0.231256051	RPL34	
1957	PROTEIN TRANSPORT PROTEIN SEC61 ALPHA SUBUNIT ISOFORM 2 (SEC61 ALPHA- 2). [Source:SWISSPROT;Acc:Q9Y2R3]	1.30722	5.6527	0.23125586	SEC61A2	
1958	"60S RIBOSOMAL PROTEIN L12, MITOCHONDRIAL PRECURSOR (L12MT) (5C5-2). [Source:SWISSPROT;Acc:P52815]"	1.09511	4.73611	0.231225626	MRPL12	
1959	NUDIX (NUCLEOSIDE DIPHOSPHATE LINKED MOIETY X)-TYPE MOTIF 12. [Source:RefSeq;Acc:NM_031438]	0.0196941	0.085173	0.231224684	NUDT12	
1960	PROTEIN 1-4 (ATP BINDING PROTEIN ASSOCIATED WITH CELL DIFFERENTIATION). [Source:SWISSPROT;Acc:O14530]	0.0389372	0.1684	0.231218527	TXNDC9	
1961	ZINC FINGER PROTEIN 291. [Source:SWISSPROT;Acc:Q9BY12]	0.0194686	0.0842001	0.231218253	SCAPER	
1962	GTP:AMP PHOSPHOTRANSFERASE MITOCHONDRIAL (EC 2.7.4.10) (AK3) (ADENYLATE KINASE 3 ALPHA LIKE 1). [Source:SWISSPROT;Acc:Q9UIJ7]	0.422914	1.82907	0.231218051	AK3	
1963		0.0194686	0.0842002	0.231217978	MED11	
1964	PEROXISOME BIOGENESIS FACTOR 1 (PEROXIN-1) (PEROXISOME BIOGENESIS DISORDER PROTEIN 1). [Source:SWISSPROT;Acc:O43933]	0.0194686	0.0842002	0.231217978	PEX1	
1965	UMP-CMP KINASE (EC 2.7.4.14) (CYTIDYLATE KINASE) (DEOXYCYTIDYLATE KINASE) (CYTIDINE MONOPHOSPHATE KINASE). [Source:SWISSPROT;Acc:P30085]	0.403445	1.74487	0.231217798	CMPK	
1966	SURFEIT LOCUS PROTEIN 5. [Source:SWISSPROT;Acc:Q15528]	0.0936292	0.40494	0.231217464	MED22	
1967	"ADENYLATE KINASE ISOENZYME 4, MITOCHONDRIAL (EC 2.7.4.3) (ATP-AMP TRANSPHOSPHORYLASE). [Source:SWISSPROT;Acc:P27144]"	0.355425	1.53719	0.231217351		
1968	60S RIBOSOMAL PROTEIN L5. [Source:SWISSPROT;Acc:P46777]	1.41778	6.13294	0.231174608	RPL5	
1969	DNA-DIRECTED RNA POLYMERASE III LARGEST SUBUNIT (EC 2.7.7.6) (RPC155) (RPC1). [Source:SWISSPROT;Acc:O14802]	0.677997	2.9329	0.231169491	POLR3A	
1970	40S RIBOSOMAL PROTEIN S9. [Source:SWISSPROT;Acc:P46781]	0.305347	1.32095	0.231157122	RPS9	
1971	60S RIBOSOMAL PROTEIN L30. [Source:SWISSPROT;Acc:P04645]	0.177407	0.767511	0.231145873	RPL30	
1972	RNA POLYMERASE I ASSOCIATED FACTOR 53. [Source:RefSeq;Acc:NM_022490]	0.0824177	0.356578	0.231135123	POLR1E	
1973	DNA REPAIR PROTEIN RAD51 HOMOLOG 1 (HRAD51) (HSRAD51). [Source:SWISSPROT;Acc:Q06609]	0.407104	1.76144	0.231119993	RAD51	
1974	KCCR13L. [Source:RefSeq;Acc:NM_139179]	0.0305909	0.13236	0.231118918	DAGLB	
1975		0.023532	0.101818	0.23111827	DAGLA	
1976	DNA POLYMERASE DELTA P38 SUBUNIT. [Source:RefSeq;Acc:NM_015584]	0.0281946	0.122012	0.231080549	POLDIP2	
1977	"ATP-DEPENDENT CLP PROTEASE ATP-BINDING SUBUNIT CLPX-LIKE, MITOCHONDRIAL PRECURSOR. [Source:SWISSPROT;Acc:O76031]"	0.139859	0.605241	0.231079851	CLPX	
1978	MITOCHONDRIAL RIBOSOMAL PROTEIN L17; LYST-INTERACTING PROTEIN LIP2. [Source:RefSeq;Acc:NM_022061]	1.18829	5.14358	0.231023917	MRPL17	
1979	60S RIBOSOMAL PROTEIN L10A (CSA-19). [Source:SWISSPROT;Acc:P53025]	0.541146	2.34239	0.231023015		
1980	"60S RIBOSOMAL PROTEIN L36, MITOCHONDRIAL PRECURSOR (L36MT) (BRCA1- INTERACTING PROTEIN 1). [Source:SWISSPROT;Acc:Q9P0J6]"	1.23017	5.32517	0.231010465	MRPL36	
1981	60S RIBOSOMAL PROTEIN L10 (QM PROTEIN) (TUMOR SUPPRESSOR QM) (LAMININ RECEPTOR HOMOLOG). [Source:SWISSPROT;Acc:P27635]	1.03026	4.4602	0.230989642		
1982	RIBOSOMAL PROTEIN L10-LIKE PROTEIN. [Source:RefSeq;Acc:NM_080746]	1.00219	4.3387	0.230988545	RPL10L	
1983	DNA-DIRECTED RNA POLYMERASE I LARGEST SUBUNIT (EC 2.7.7.6) (RNA POLYMERASE I 194 KDA SUBUNIT) (RPA194). [Source:SWISSPROT;Acc:O95602]	0.661854	2.86554	0.230970079	POLR1A	
1984	EPOXIDE HYDROLASE 1 (EC 3.3.2.3) (MICROSOMAL EPOXIDE HYDROLASE) (EPOXIDE HYDRATASE). [Source:SWISSPROT;Acc:P07099]	0.160147	0.693413	0.230954712	EPHX1	
1985	"28S RIBOSOMAL PROTEIN S12, MITOCHONDRIAL PRECURSOR (MPR-S12) (MT- RPS12). [Source:SWISSPROT;Acc:O15235]"	0.485913	2.1041	0.230936267	MRPS12	
1986	40S RIBOSOMAL PROTEIN S23. [Source:SWISSPROT;Acc:P39028]	0.485913	2.1041	0.230936267	RPS23	
1987	60S RIBOSOMAL PROTEIN L12. [Source:SWISSPROT;Acc:P30050]	0.527851	2.28589	0.230917061		
1988	DJ999L4.1 (NOVEL PROTEIN SIMILAR TO RIBOSOMAL PROTEIN L12 (RPL12)). [Source:SPTREMBL;Acc:Q9NQ02]	0.512921	2.22124	0.230916515		
1989	60S RIBOSOMAL PROTEIN L12 LIKE PROTEIN. [Source:SPTREMBL;Acc:O60886]	0.505323	2.18834	0.230916128		
1990	DNA-DIRECTED RNA POLYMERASE II LARGEST SUBUNIT (EC 2.7.7.6) (RPB1). [Source:SWISSPROT;Acc:P24928]	0.525129	2.27455	0.230871601	POLR2A	
1991	HYALURONAN SYNTHASE 3 (EC 2.4.1.212) (HYALURONATE SYNTHASE 3) (HYALURONIC ACID SYNTHASE 3) (HA SYNTHASE 3). [Source:SWISSPROT;Acc:O00219]	0.0223215	0.0966924	0.230850615	HAS3	
1992	HYALURONAN SYNTHASE 1 (EC 2.4.1.212) (HYALURONATE SYNTHASE 1) (HYALURONIC ACID SYNTHASE 1) (HA SYNTHASE 1) (HUHAS1). [Source:SWISSPROT;Acc:Q92839]	0.0190828	0.0826631	0.230850283	HAS1	
1993	HYALURONAN SYNTHASE 2 (EC 2.4.1.212) (HYALURONATE SYNTHASE 2) (HYALURONIC ACID SYNTHASE 2) (HA SYNTHASE 2). [Source:SWISSPROT;Acc:Q92819]	0.0203563	0.0881799	0.230849661	HAS2	
1994		0.22609	0.979382	0.230849658	DOHH	
1995	INTEGRAL MEMBRANE PROTEIN CII-3B. [Source:SPTREMBL;Acc:O75609]	0.221383	0.959291	0.230777731		
1996	"SUCCINATE DEHYDROGENASE CYTOCHROME B560 SUBUNIT, MITOCHONDRIAL PRECURSOR (INTEGRAL MEMBRANE PROTEIN CII-3) (QPS1) (QPS-1) (SUCCINATE DEHYDROGENASE COMPLEX SUBUNIT C) (SUCCINATE-UBIQUINONE OXIDOREDUCTASE CYTOCHROME B LARGE SUBUNIT) (CYBL). [Source:SWISSPRO"	0.240428	1.04189	0.230761405	SDHC	
1997	40S RIBOSOMAL PROTEIN S14 (PRO2640). [Source:SWISSPROT;Acc:P06366]	0.543161	2.35379	0.230760178	RPS14	
1998	40S RIBOSOMAL PROTEIN S18 (KE-3) (KE3). [Source:SWISSPROT;Acc:P25232]	0.543161	2.35379	0.230760178		
1999	METHIONINE AMINOPEPTIDASE 1 (EC 3.4.11.18) (METAP 1) (MAP 1) (PEPTIDASE M 1). [Source:SWISSPROT;Acc:P53582]	0.445085	1.92889	0.230746699	METAP1	
2000	METHIONINE AMINOPEPTIDASE 2 (EC 3.4.11.18) (METAP 2) (PEPTIDASE M 2) (INITIATION FACTOR 2 ASSOCIATED 67 KDA GLYCOPROTEIN) (P67) (P67EIF2). [Source:SWISSPROT;Acc:P50579]	0.445085	1.92889	0.230746699	METAP2	
2001	POLY (ADP-RIBOSE) GLYCOHYDROLASE. [Source:RefSeq;Acc:NM_003631]	0.0320499	0.138898	0.230744143		

Legend:
- Rank is the rank after comparing the two networks
- Hugo is the bloody hugo identifier as demanded by the BMC Bioinformatics idiots

- http://analysis.yellowcouch.org/