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 2658 to 2707 of 3206 in total

Rank	description	measured	expected	final	Hugo	
2658	"SOLUTE CARRIER FAMILY 13, MEMBER 4 (NA+/SULFATE COTRANSPORTER SUT-1). [Source:SWISSPROT;Acc:Q9UKG4]"	0.0480531	0.228892	0.209937875	SLC13A4	
2659	"SOLUTE CARRIER FAMILY 13, MEMBER 1 (RENAL SODIUM/SULFATE COTRANSPORTER) (NA(+)/SULFATE COTRANSPORTER) (HNASI-1). [Source:SWISSPROT;Acc:Q9BZW2]"	0.0481673	0.229436	0.209937848	SLC13A1	
2660	"SOLUTE CARRIER FAMILY 13, MEMBER 2 (RENAL SODIUM/DICARBOXYLATE COTRANSPORTER) (NA(+)/DICARBOXYLATE COTRANSPORTER 1) (NADC-1). [Source:SWISSPROT;Acc:Q13183]"	0.0401827	0.191403	0.209937671	SLC13A2	
2661	PHOSPHATIDATE CYTIDYLYLTRANSFERASE 1 (EC 2.7.7.41) (CDP-DIGLYCERIDE SYNTHETASE 1) (CDP-DIGLYCERIDE PYROPHOSPHORYLASE 1) (CDP- DIACYLGLYCEROL SYNTHASE 1) (CDS 1) (CTP:PHOSPHATIDATE CYTIDYLYLTRANSFERASE 1) (CDP-DAG SYNTHASE 1) (CDP-DG SYNTHETASE 1). [Source	0.558539	2.66089	0.209906836	CDS1	
2662	"ELECTRON TRANSFER FLAVOPROTEIN-UBIQUINONE OXIDOREDUCTASE, MITOCHONDRIAL PRECURSOR (EC 1.5.5.1) (ETF-QO) (ETF-UBIQUINONE OXIDOREDUCTASE) (ETF DEHYDROGENASE) (ELECTRON-TRANSFERRING- FLAVOPROTEIN DEHYDROGENASE). [Source:SWISSPROT;Acc:Q16134]"	0.114957	0.548489	0.209588524	ETFDH	
2663	POLYMYOSITIS/SCLERODERMA AUTOANTIGEN 2 (AUTOANTIGEN PM/SCL 2) (POLYMYOSITIS/SCLERODERMA AUTOANTIGEN 100 KDA) (PM/SCL-100) (P100 POLYMYOSITIS-SCLERODERMA OVERLAP SYNDROME ASSOCIATED AUTOANTIGEN). [Source:SWISSPROT;Acc:Q01780]	0.474956	2.26784	0.209431	EXOSC10	
2664	DEOXYCYTIDYLATE DEAMINASE (EC 3.5.4.12) (DCMP DEAMINASE). [Source:SWISSPROT;Acc:P32321]	0.124149	0.593022	0.209349737	DCTD	
2665	ASPARTYL-TRNA SYNTHETASE (EC 6.1.1.12) (ASPARTATE--TRNA LIGASE) (ASPRS). [Source:SWISSPROT;Acc:P14868]	0.149127	0.712692	0.209244667	DARS	
2666	NEURAL CELL ADHESION MOLECULE L1 PRECURSOR (N-CAM L1) (CD171 ANTIGEN). [Source:SWISSPROT;Acc:P32004]	0.02527	0.120774	0.209233775		
2667	TRANSCRIPTION FACTOR MAFF (V-MAF MUSCULOAPONEUROTIC FIBROSARCOMA ONCOGENE HOMOLOG F) (U-MAF). [Source:SWISSPROT;Acc:Q9ULX9]	0.0761231	0.363819	0.209233438	MAFF	
2668	NUCLEAR FACTOR (ERYTHROID-DERIVED 2)-LIKE 3; NF-E2-RELATED FACTOR 3. [Source:RefSeq;Acc:NM_004289]	0.0877868	0.419564	0.209233395	NFE2L3	
2669	TRANSCRIPTION INITIATION FACTOR TFIID 31 KDA SUBUNIT (TAFII-31) (TAFII-32) (TAFII32). [Source:SWISSPROT;Acc:Q16594]	0.61918	2.95928	0.209233327	TAF9	
2670	TRANSCRIPTION FACTOR MAFG (V-MAF MUSCULOAPONEUROTIC FIBROSARCOMA ONCOGENE HOMOLOG G) (HMAF). [Source:SWISSPROT;Acc:O15525]	0.0798317	0.381544	0.209233273		
2671	"NUCLEAR FACTOR ERYTHROID 2 RELATED FACTOR 1 (NF-E2 RELATED FACTOR 1) (NFE2-RELATED FACTOR 1) (NUCLEAR FACTOR, ERYTHROID DERIVED 2, LIKE 1) (TRANSCRIPTION FACTOR 11) (TRANSCRIPTION FACTOR HBZ17) (TRANSCRIPTION FACTOR LCR-F1) (LOCUS CONTROL REGION-FACTOR 1)"	0.0693641	0.331516	0.209233039	NFE2L1	
2672	TRANSCRIPTION FACTOR MAFK (ERYTHROID TRANSCRIPTION FACTOR NF-E2 P18 SUBUNIT). [Source:SWISSPROT;Acc:O60675]	0.0897053	0.428734	0.209232998		
2673		0.0251255	0.120084	0.209232704	NFASC	
2674	CELL ADHESION MOLECULE WITH HOMOLOGY TO L1CAM PRECURSOR; NEURAL CELL ADHESION MOLECULE; CELL ADHESION MOLECULE L1-LIKE; L1 CELL ADHESION MOLECULE 2. [Source:RefSeq;Acc:NM_006614]	0.0249248	0.119125	0.209232319	CHL1	
2675	"TBP-ASSOCIATED FACTOR 9L; NEURONAL CELL DEATH-RELATED PROTEIN; TAF9-LIKE RNA POLYMERASE II, TATA BOX BINDING PROTEIN (TBP)-ASSOCIATED FACTOR, 31 KD; NEURONAL CELL DEATH-RELATED GENE IN NEURON-7; TRANSCRIPTION ASSOCIATED FACTOR TAFII31L; TRANSCRIPTION INIT"	0.383112	1.83532	0.208743979	TAF9B	
2676	N-ACETYLGALACTOSAMINE KINASE (EC 2.7.1.-) (GALNAC KINASE) (GALACTOKINASE 2). [Source:SWISSPROT;Acc:Q01415]	0.0435693	0.20874	0.208725208	GALK2	
2677	GALACTOSE-1-PHOSPHATE URIDYLYLTRANSFERASE (EC 2.7.7.12) (GAL-1-P URIDYLYLTRANSFERASE) (UDP-GLUCOSE--HEXOSE-1-PHOSPHATE URIDYLYLTRANSFERASE). [Source:SWISSPROT;Acc:P07902]	0.0454701	0.217847	0.208724931		
2678	UDP-GLUCOSE 4-EPIMERASE (EC 5.1.3.2) (GALACTOWALDENASE) (UDP- GALACTOSE 4-EPIMERASE). [Source:SWISSPROT;Acc:Q14376]	0.234953	1.12566	0.208724659	GALE	
2679	"ACYL-COENZYME A OXIDASE 2, PEROXISOMAL (EC 1.3.3.6) (BRANCHED-CHAIN ACYL-COA OXIDASE) (BRCACOX) (TRIHYDROXYCOPROSTANOYL-COA OXIDASE) (THCCOX) (THCA-COA OXIDASE). [Source:SWISSPROT;Acc:Q99424]"	0.663483	3.18084	0.208587354	ACOX2	
2680	POLY(A) POLYMERASE GAMMA (EC 2.7.7.19) (PAP GAMMA) (POLYNUCLEOTIDE ADENYLYLTRANSFERASE GAMMA) (SRP RNA 3' ADENYLATING ENZYME). [Source:SWISSPROT;Acc:Q9BWT3]	0.377523	1.81111	0.20844841	PAPOLG	
2681	MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 7 INTERACTING PROTEIN 1 (TAK1-BINDING PROTEIN 1). [Source:SWISSPROT;Acc:Q15750]	0.225506	1.08199	0.208417823	MAP3K7IP1	
2682	EXOCYST COMPLEX COMPONENT SEC5. [Source:SWISSPROT;Acc:Q96KP1]	0.0545554	0.261799	0.208386587	EXOC2	
2683	RETICULON PROTEIN 3 (NEUROENDOCRINE-SPECIFIC PROTEIN-LIKE 2) (NSP-LIKE PROTEIN II) (NSPLII). [Source:SWISSPROT;Acc:O95197]	0.203468	0.976589	0.208345578	RTN3	
2684	POLY(A) POLYMERASE ALPHA (EC 2.7.7.19) (PAP) (POLYNUCLEOTIDE ADENYLYLTRANSFERASE ALPHA) (FRAGMENT). [Source:SWISSPROT;Acc:P51003]	0.438432	2.10446	0.20833468	PAPOLA	
2685	RETICULON PROTEIN 2 (NEUROENDOCRINE-SPECIFIC PROTEIN-LIKE 1) (NSP-LIKE PROTEIN 1) (NSPLI). [Source:SWISSPROT;Acc:O75298]	0.175589	0.842838	0.208330664	RTN2	
2686	EH-DOMAIN CONTAINING PROTEIN 1 (TESTILIN) (HPAST1). [Source:SWISSPROT;Acc:Q9H4M9]	0.121	0.580932	0.208285996	EHD1	
2687	EH-DOMAIN CONTAINING PROTEIN 3. [Source:SWISSPROT;Acc:Q9NZN3]	0.107786	0.517492	0.208285345	EHD3	
2688	EH-DOMAIN CONTAINING PROTEIN 4 (EH DOMAIN-CONTAINING PROTEIN FKSG7) (HEPATOCELLULAR CARCINOMA-ASSOCIATED PROTEIN 10/11). [Source:SWISSPROT;Acc:Q9H223]	0.0943663	0.453066	0.208283782	EHD4	
2689	EH-DOMAIN CONTAINING PROTEIN 2. [Source:SWISSPROT;Acc:Q9NZN4]	0.0892656	0.428577	0.208283692	EHD2	
2690	SIN3 ASSOCIATED POLYPEPTIDE P18 (2HOR0202). [Source:SWISSPROT;Acc:O00422]	0.0937258	0.450013	0.208273539	SAP18	
2691	RETICULON 1 (NEUROENDOCRINE-SPECIFIC PROTEIN). [Source:SWISSPROT;Acc:Q16799]	0.268811	1.29069	0.20826922	RTN1	
2692	RETICULON 4 (NEURITE OUTGROWTH INHIBITOR) (NOGO PROTEIN) (FOOCEN) (NEUROENDOCRINE-SPECIFIC PROTEIN) (NSP) (NEUROENDOCRINE SPECIFIC PROTEIN C HOMOLOG) (RTN-X) (RETICULON 5) (MY043 PROTEIN). [Source:SWISSPROT;Acc:Q9NQC3]	0.267978	1.28698	0.20822235	RTN4	
2693		0.122185	0.586832	0.208211209	AIFM3	
2694	"STEROID HORMONE RECEPTOR ERR1 (ESTROGEN-RELATED RECEPTOR, ALPHA) (ERR-ALPHA) (ESTROGEN RECEPTOR-LIKE 1). [Source:SWISSPROT;Acc:P11474]"	0.13519	0.649418	0.208171009	ESRRA	
2695	T-BOX TRANSCRIPTION FACTOR TBX6 (T-BOX PROTEIN 6). [Source:SWISSPROT;Acc:O95947]	0.018755	0.0901743	0.207986089	TBX6	
2696	"ENDONUCLEASE G, MITOCHONDRIAL PRECURSOR (EC 3.1.30.-) (ENDO G). [Source:SWISSPROT;Acc:Q14249]"	0.0410294	0.19727	0.207986009	ENDOG	
2697	"PROGRAMMED CELL DEATH PROTEIN 8, MITOCHONDRIAL PRECURSOR (EC 1.-.-.-) (APOPTOSIS-INDUCING FACTOR). [Source:SWISSPROT;Acc:O95831]"	0.112229	0.5396	0.207985545	AIFM1	
2698	ESTROGEN-RELATED RECEPTOR GAMMA (ESTROGEN RECEPTOR RELATED PROTEIN 3) (ERR GAMMA-2). [Source:SWISSPROT;Acc:O75454]	0.151787	0.730409	0.207810966		
2699	HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN L (HNRNP L). [Source:SWISSPROT;Acc:P14866]	0.100335	0.482909	0.207772065	HNRNPL	
2700		0.0804074	0.387009	0.207766228	HNRPLL	
2701	METAXIN 1. [Source:SWISSPROT;Acc:Q13505]	0.133976	0.645054	0.20769734	MTX1	
2702		0.145039	0.698388	0.207676821	FAM82B	
2703	MONOGLYCERIDE LIPASE; LYSOPHOSPHOLIPASE-LIKE. [Source:RefSeq;Acc:NM_007283]	0.0986882	0.475276	0.207643979	MGLL	
2704	"CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR, 73 KDA SUBUNIT (CPSF 73 KDA SUBUNIT). [Source:SWISSPROT;Acc:Q9UKF6]"	0.412088	1.98586	0.207511104	CPSF3	
2705		0.119287	0.574873	0.207501483	ABHD14B	
2706	"STEROID HORMONE RECEPTOR ERR2 (ESTROGEN-RELATED RECEPTOR, BETA) (ERR-BETA) (ESTROGEN RECEPTOR-LIKE 2) (ERR BETA-2). [Source:SWISSPROT;Acc:O95718]"	0.175846	0.847805	0.207413261	ESRRB	
2707		0.542979	2.61855	0.207358653		

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/