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 2002 to 2051 of 3206 in total

Rank	description	measured	expected	final	Hugo	
2002		0.029603	0.128294	0.230743449		
2003		0.0937028	0.406091	0.230743356	TXNDC10	
2004	MTO1 PROTEIN HOMOLOG (CGI-02). [Source:SWISSPROT;Acc:Q9Y2Z2]	0.297474	1.2892	0.230743096	MTO1	
2005	40S RIBOSOMAL PROTEIN S20. [Source:SWISSPROT;Acc:P17075]	0.834926	3.6186	0.230731775	RPS20	
2006	"HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-9 SPECIFIC 1 (EC 2.1.1.43) (HISTONE H3-K9 METHYLTRANSFERASE 1) (H3-K9-HMTASE 1) (SUPPRESSOR OF VARIEGATION 3-9 HOMOLOG 1) (SU(VAR)3-9 HOMOLOG 1). [Source:SWISSPROT;Acc:O43463]"	0.027437	0.118935	0.230689032	SUV39H1	
2007	EUKARYOTIC TRANSLATION INITIATION FACTOR 2 SUBUNIT 1 (EUKARYOTIC TRANSLATION INITIATION FACTOR 2 ALPHA SUBUNIT) (EIF-2-ALPHA) (EIF- 2ALPHA) (EIF-2A). [Source:SWISSPROT;Acc:P05198]	0.761536	3.30114	0.230688792	EIF2S1	
2008	"HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-9 SPECIFIC 2 (EC 2.1.1.43) (HISTONE H3-K9 METHYLTRANSFERASE 2) (H3-K9-HMTASE 2) (SUPPRESSOR OF VARIEGATION 3-9 HOMOLOG 2) (SU(VAR)3-9 HOMOLOG 2). [Source:SWISSPROT;Acc:Q9H5I1]"	0.0323264	0.14013	0.230688646	SUV39H2	
2009	NUCLEOSIDE DIPHOSPHATE KINASE B (EC 2.7.4.6) (NDK B) (NDP KINASE B) (NM23-H2) (C-MYC PURINE-BINDING TRANSCRIPTION FACTOR PUF). [Source:SWISSPROT;Acc:P22392]	0.533964	2.31472	0.230681897		
2010	NUCLEOSIDE DIPHOSPHATE KINASE A (EC 2.7.4.6) (NDK A) (NDP KINASE A) (TUMOR METASTATIC PROCESS-ASSOCIATED PROTEIN) (METASTASIS INHIBITION FACTOR NM23) (NM23-H1). [Source:SWISSPROT;Acc:P15531]	0.494361	2.14316	0.230669199	NME2	
2011	PUTATIVE NUCLEOSIDE DIPHOSPHATE KINASE (EC 2.7.4.6) (NDK) (NDP KINASE). [Source:SWISSPROT;Acc:O60361]	0.480816	2.08449	0.230663616	NME2P1	
2012	40S RIBOSOMAL PROTEIN S2 (S4) (LLREP3 PROTEIN). [Source:SWISSPROT;Acc:P15880]	1.469	6.36963	0.230625641		
2013	PROTEIN ARGININE N-METHYLTRANSFERASE 3 (EC 2.1.1.-) (FRAGMENT). [Source:SWISSPROT;Acc:O60678]	0.0198445	0.0860464	0.230625569	PRMT3	
2014	60S RIBOSOMAL PROTEIN L23 (L17). [Source:SWISSPROT;Acc:P23131]	0.64348	2.79016	0.230624767		
2015	BRCA2 AND CDKN1A-INTERACTING PROTEIN ISOFORM BCCIPALPHA; BRCA2 AND CDKN1A-INTERACTING PROTEIN; CDK INHIBITOR P21 BINDING PROTEIN; BCCIPALPHA; BCCIPBETA; TOK-1ALPHA; TOK-1BETA. [Source:RefSeq;Acc:NM_016567]	0.0167203	0.0725001	0.230624509	BCCIP	
2016	PUTATIVE EUKARYOTIC TRANSLATION INITIATION FACTOR 1A (EIF-1A) (EIF- 4C). [Source:SWISSPROT;Acc:O75642]	1.27676	5.53686	0.230592791		
2017	"SUCCINATE DEHYDROGENASE [UBIQUINONE] IRON-SULFUR PROTEIN, MITOCHONDRIAL PRECURSOR (EC 1.3.5.1) (IP) (IRON-SULFUR SUBUNIT OF COMPLEX II). [Source:SWISSPROT;Acc:P21912]"	0.311095	1.34923	0.230572252	SDHB	
2018	40S RIBOSOMAL PROTEIN S16. [Source:SWISSPROT;Acc:P17008]	0.590899	2.56327	0.230525462	RPS16	
2019	"60S RIBOSOMAL PROTEIN L13, MITOCHONDRIAL (L13MT). [Source:SWISSPROT;Acc:Q9BYD1]"	0.590899	2.56327	0.230525462	MRPL13	
2020	60S RIBOSOMAL PROTEIN L13A (23 KDA HIGHLY BASIC PROTEIN). [Source:SWISSPROT;Acc:P40429]	0.587935	2.55045	0.230522065	RPL13A	
2021	"LON PROTEASE HOMOLOG, MITOCHONDRIAL PRECURSOR (EC 3.4.21.-) (LON PROTEASE-LIKE PROTEIN) (LONP) (LONHS). [Source:SWISSPROT;Acc:P36776]"	0.0840355	0.364571	0.230505169		
2022		0.123498	0.535804	0.230491	C11orf79	
2023	"MAGUK P55 SUBFAMILY MEMBER 3 (MPP3 PROTEIN) (DISCS, LARGE HOMOLOG 3). [Source:SWISSPROT;Acc:Q13368]"	0.112993	0.490447	0.230387789	MPP3	
2024	TRANSKETOLASE (EC 2.2.1.1) (TK). [Source:SWISSPROT;Acc:P29401]	0.150764	0.654499	0.230350237	TKT	
2025	"PYRUVATE DEHYDROGENASE E1 COMPONENT ALPHA SUBUNIT, SOMATIC FORM, MITOCHONDRIAL PRECURSOR (EC 1.2.4.1) (PDHE1-A TYPE I). [Source:SWISSPROT;Acc:P08559]"	0.38076	1.65321	0.230315568	PDHA1	
2026		0.0327033	0.142004	0.230298442	C3orf23	
2027		0.0370628	0.160934	0.230298135	SIN3B	
2028	DENSITY-REGULATED PROTEIN (DRP) (DRP1 PROTEIN) (SMOOTH MUSCLE CELL ASSOCIATED PROTEIN-3) (SMAP-3). [Source:SWISSPROT;Acc:O43583]	0.469395	2.03821	0.230297663	DENR	
2029	"TRANSCRIPTIONAL CO-REPRESSOR SIN3A; TRANSCRIPTIONAL REGULATOR, SIN3A (YEAST). [Source:RefSeq;Acc:NM_015477]"	0.0283438	0.123075	0.230296973	SIN3A	
2030	"PYRUVATE DEHYDROGENASE E1 COMPONENT ALPHA SUBUNIT, TESTIS-SPECIFIC FORM, MITOCHONDRIAL PRECURSOR (EC 1.2.4.1) (PDHE1-A TYPE II). [Source:SWISSPROT;Acc:P29803]"	0.353795	1.53626	0.230296304	PDHA2	
2031	PROTEIN TRANSPORT PROTEIN SEC61 GAMMA SUBUNIT. [Source:SWISSPROT;Acc:P38384]	0.114962	0.499271	0.230259719	SEC61G	
2032		0.116403	0.505621	0.23021789		
2033	TRNA PSEUDOURIDINE SYNTHASE A (EC 4.2.1.70) (PSEUDOURIDYLATE SYNTHASE I) (PSEUDOURIDINE SYNTHASE I) (URACIL HYDROLYASE). [Source:SWISSPROT;Acc:Q9Y606]	0.474475	2.06115	0.230199161	PUS1	
2034		0.473995	2.05907	0.230198585	PUS3	
2035		0.0841705	0.365653	0.230192286	DARS2	
2036	40S RIBOSOMAL PROTEIN S5. [Source:SWISSPROT;Acc:P46782]	1.08774	4.7257	0.230175424	RPS5	
2037	CASEIN KINASE I ALPHA S-LIKE. [Source:RefSeq;Acc:NM_145203]	0.0896146	0.389336	0.23017291	CSNK1A1L	
2038	"CASEIN KINASE I, ALPHA ISOFORM (EC 2.7.1.-) (CKI-ALPHA) (CK1). [Source:SWISSPROT;Acc:P48729]"	0.0909346	0.395071	0.230172804	CSNK1A1	
2039	HUNTINGTIN INTERACTING PROTEIN 1 RELATED (HIP1-RELATED) (HIP 12). [Source:SWISSPROT;Acc:O75146]	0.127824	0.555396	0.230149299	HIP1R	
2040	"40S RIBOSOMAL PROTEIN S4, X ISOFORM (SINGLE COPY ABUNDANT MRNA PROTEIN) (SCR10). [Source:SWISSPROT;Acc:P12750]"	0.707942	3.07604	0.230147202		
2041	"40S RIBOSOMAL PROTEIN S4, Y ISOFORM 2. [Source:SWISSPROT;Acc:Q8TD47]"	0.667613	2.90083	0.23014551	RPS4Y2	
2042	GOODPASTURE ANTIGEN-BINDING PROTEIN (EC 2.7.1.37) (GPBP) (COLLAGEN TYPE IV ALPHA 3 BINDING PROTEIN) (STAR-RELATED LIPID TRANSFER PROTEIN 11) (STARD11) (START DOMAIN-CONTAINING PROTEIN 11). [Source:SWISSPROT;Acc:Q9Y5P4]	0.0646597	0.280961	0.230137635	COL4A3BP	
2043	HUNTINGTIN INTERACTING PROTEIN 1 (HIP-I). [Source:SWISSPROT;Acc:O00291]	0.104281	0.453153	0.230123159	HIP1	
2044	DNA-DIRECTED RNA POLYMERASE II 14.5 KDA POLYPEPTIDE (EC 2.7.7.6) (RPB9) (RPB14.5). [Source:SWISSPROT;Acc:P36954]	0.110371	0.479632	0.230116006	POLR2I	
2045	U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM4 (GLYCINE-RICH PROTEIN) (GRP). [Source:SWISSPROT;Acc:Q9Y4Z0]	0.308754	1.34189	0.230088904	LSM4	
2046	DNA-DIRECTED RNA POLYMERASE I 40 KDA POLYPEPTIDE (EC 2.7.7.6) (RPA40) (RPA39). [Source:SWISSPROT;Acc:O15160]	1.55851	6.77601	0.230004088	POLR1C	
2047	INORGANIC PYROPHOSPHATASE 2 ISOFORM 1. [Source:RefSeq;Acc:NM_176869]	0.123888	0.538763	0.229948976	PPA2	
2048	AH RECEPTOR-INTERACTING PROTEIN (AIP) (IMMUNOPHILIN HOMOLOG ARA9) (HBV-X ASSOCIATED PROTEIN 2). [Source:SWISSPROT;Acc:O00170]	0.052087	0.226516	0.229948436	AIP	
2049	INORGANIC PYROPHOSPHATASE (EC 3.6.1.1) (PYROPHOSPHATE PHOSPHO- HYDROLASE) (PPASE). [Source:SWISSPROT;Acc:Q15181]	0.128098	0.557073	0.229948319	PPA1	
2050	ARYL-HYDROCARBON INTERACTING PROTEIN-LIKE 1. [Source:SWISSPROT;Acc:Q9NZN9]	0.0410498	0.178518	0.22994768	AIPL1	
2051	"COMPLEMENT COMPONENT 1, Q SUBCOMPONENT BINDING PROTEIN, MITOCHONDRIAL PRECURSOR (GLYCOPROTEIN GC1QBP) (GC1Q-R PROTEIN) (HYALURONAN-BINDING PROTEIN 1) (P32) (P33). [Source:SWISSPROT;Acc:Q07021]"	0.532733	2.31678	0.229945442	C1QBP	

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/