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 Hugo measured expected final

Results: HTML CSV LaTeX

Showing element 2002 to 2051 of 3206 in total

Rank	description	Hugo	measured	expected	final	
2002			0.029603	0.128294	0.230743449	
2003		TXNDC10	0.0937028	0.406091	0.230743356	
2004	MTO1 PROTEIN HOMOLOG (CGI-02). [Source:SWISSPROT;Acc:Q9Y2Z2]	MTO1	0.297474	1.2892	0.230743096	
2005	40S RIBOSOMAL PROTEIN S20. [Source:SWISSPROT;Acc:P17075]	RPS20	0.834926	3.6186	0.230731775	
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]"	SUV39H1	0.027437	0.118935	0.230689032	
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]	EIF2S1	0.761536	3.30114	0.230688792	
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]"	SUV39H2	0.0323264	0.14013	0.230688646	
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]	NME2	0.494361	2.14316	0.230669199	
2011	PUTATIVE NUCLEOSIDE DIPHOSPHATE KINASE (EC 2.7.4.6) (NDK) (NDP KINASE). [Source:SWISSPROT;Acc:O60361]	NME2P1	0.480816	2.08449	0.230663616	
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]	PRMT3	0.0198445	0.0860464	0.230625569	
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]	BCCIP	0.0167203	0.0725001	0.230624509	
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]"	SDHB	0.311095	1.34923	0.230572252	
2018	40S RIBOSOMAL PROTEIN S16. [Source:SWISSPROT;Acc:P17008]	RPS16	0.590899	2.56327	0.230525462	
2019	"60S RIBOSOMAL PROTEIN L13, MITOCHONDRIAL (L13MT). [Source:SWISSPROT;Acc:Q9BYD1]"	MRPL13	0.590899	2.56327	0.230525462	
2020	60S RIBOSOMAL PROTEIN L13A (23 KDA HIGHLY BASIC PROTEIN). [Source:SWISSPROT;Acc:P40429]	RPL13A	0.587935	2.55045	0.230522065	
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		C11orf79	0.123498	0.535804	0.230491	
2023	"MAGUK P55 SUBFAMILY MEMBER 3 (MPP3 PROTEIN) (DISCS, LARGE HOMOLOG 3). [Source:SWISSPROT;Acc:Q13368]"	MPP3	0.112993	0.490447	0.230387789	
2024	TRANSKETOLASE (EC 2.2.1.1) (TK). [Source:SWISSPROT;Acc:P29401]	TKT	0.150764	0.654499	0.230350237	
2025	"PYRUVATE DEHYDROGENASE E1 COMPONENT ALPHA SUBUNIT, SOMATIC FORM, MITOCHONDRIAL PRECURSOR (EC 1.2.4.1) (PDHE1-A TYPE I). [Source:SWISSPROT;Acc:P08559]"	PDHA1	0.38076	1.65321	0.230315568	
2026		C3orf23	0.0327033	0.142004	0.230298442	
2027		SIN3B	0.0370628	0.160934	0.230298135	
2028	DENSITY-REGULATED PROTEIN (DRP) (DRP1 PROTEIN) (SMOOTH MUSCLE CELL ASSOCIATED PROTEIN-3) (SMAP-3). [Source:SWISSPROT;Acc:O43583]	DENR	0.469395	2.03821	0.230297663	
2029	"TRANSCRIPTIONAL CO-REPRESSOR SIN3A; TRANSCRIPTIONAL REGULATOR, SIN3A (YEAST). [Source:RefSeq;Acc:NM_015477]"	SIN3A	0.0283438	0.123075	0.230296973	
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]"	PDHA2	0.353795	1.53626	0.230296304	
2031	PROTEIN TRANSPORT PROTEIN SEC61 GAMMA SUBUNIT. [Source:SWISSPROT;Acc:P38384]	SEC61G	0.114962	0.499271	0.230259719	
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]	PUS1	0.474475	2.06115	0.230199161	
2034		PUS3	0.473995	2.05907	0.230198585	
2035		DARS2	0.0841705	0.365653	0.230192286	
2036	40S RIBOSOMAL PROTEIN S5. [Source:SWISSPROT;Acc:P46782]	RPS5	1.08774	4.7257	0.230175424	
2037	CASEIN KINASE I ALPHA S-LIKE. [Source:RefSeq;Acc:NM_145203]	CSNK1A1L	0.0896146	0.389336	0.23017291	
2038	"CASEIN KINASE I, ALPHA ISOFORM (EC 2.7.1.-) (CKI-ALPHA) (CK1). [Source:SWISSPROT;Acc:P48729]"	CSNK1A1	0.0909346	0.395071	0.230172804	
2039	HUNTINGTIN INTERACTING PROTEIN 1 RELATED (HIP1-RELATED) (HIP 12). [Source:SWISSPROT;Acc:O75146]	HIP1R	0.127824	0.555396	0.230149299	
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]"	RPS4Y2	0.667613	2.90083	0.23014551	
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]	COL4A3BP	0.0646597	0.280961	0.230137635	
2043	HUNTINGTIN INTERACTING PROTEIN 1 (HIP-I). [Source:SWISSPROT;Acc:O00291]	HIP1	0.104281	0.453153	0.230123159	
2044	DNA-DIRECTED RNA POLYMERASE II 14.5 KDA POLYPEPTIDE (EC 2.7.7.6) (RPB9) (RPB14.5). [Source:SWISSPROT;Acc:P36954]	POLR2I	0.110371	0.479632	0.230116006	
2045	U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM4 (GLYCINE-RICH PROTEIN) (GRP). [Source:SWISSPROT;Acc:Q9Y4Z0]	LSM4	0.308754	1.34189	0.230088904	
2046	DNA-DIRECTED RNA POLYMERASE I 40 KDA POLYPEPTIDE (EC 2.7.7.6) (RPA40) (RPA39). [Source:SWISSPROT;Acc:O15160]	POLR1C	1.55851	6.77601	0.230004088	
2047	INORGANIC PYROPHOSPHATASE 2 ISOFORM 1. [Source:RefSeq;Acc:NM_176869]	PPA2	0.123888	0.538763	0.229948976	
2048	AH RECEPTOR-INTERACTING PROTEIN (AIP) (IMMUNOPHILIN HOMOLOG ARA9) (HBV-X ASSOCIATED PROTEIN 2). [Source:SWISSPROT;Acc:O00170]	AIP	0.052087	0.226516	0.229948436	
2049	INORGANIC PYROPHOSPHATASE (EC 3.6.1.1) (PYROPHOSPHATE PHOSPHO- HYDROLASE) (PPASE). [Source:SWISSPROT;Acc:Q15181]	PPA1	0.128098	0.557073	0.229948319	
2050	ARYL-HYDROCARBON INTERACTING PROTEIN-LIKE 1. [Source:SWISSPROT;Acc:Q9NZN9]	AIPL1	0.0410498	0.178518	0.22994768	
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]"	C1QBP	0.532733	2.31678	0.229945442	

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/