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 551 to 600 of 3206 in total 
Rank	description	measured	expected	final	Hugo	
551	TBC1 DOMAIN FAMILY PROTEIN C22ORF4. [Source:SWISSPROT;Acc:Q8WUA7]	0.046789	0.172653	0.271000214	TBC1D22A	
552	NUCLEAR RECEPTOR COACTIVATOR 7; ESTROGEN RECEPTOR ASSOCIATED PROTEIN 140 KDA. [Source:RefSeq;Acc:NM_181782]	0.046789	0.172653	0.271000214	NCOA7	
553	"LATS, LARGE TUMOR SUPPRESSOR, HOMOLOG 2; LATS (LARGE TUMOR SUPPRESSOR, DROSOPHILA) HOMOLOG 2. [Source:RefSeq;Acc:NM_014572]"	0.0385424	0.142223	0.270999768	LATS2	
554	SH3 DOMAIN-BINDING GLUTAMIC ACID-RICH-LIKE PROTEIN 2 (FOVEA-ASSOCIATED SH3 DOMAIN BINDING PROTEIN). [Source:SWISSPROT;Acc:Q9UJC5]	0.0368814	0.136094	0.270999456		
555	DJ132F21.2 (CONTAINS A NOVEL PROTEIN SIMILAR TO THE L82E FROM DROSOPHILA) (FRAGMENT). [Source:SPTREMBL;Acc:Q9H125]	0.0362497	0.133763	0.270999454	C20orf118	
556	SH3 DOMAIN-BINDING GLUTAMIC ACID-RICH-LIKE PROTEIN. [Source:SWISSPROT;Acc:O75368]	0.0371738	0.137173	0.270999395	SH3BGRL	
557	OXIDATION RESISTANCE 1. [Source:RefSeq;Acc:NM_181354]	0.0380979	0.140583	0.270999338	OXR1	
558	DYMECLIN. [Source:RefSeq;Acc:NM_017653]	0.50366	1.85853	0.270999123	DYM	
559	TBC1 DOMAIN FAMILY PROTEIN C22ORF4-LIKE (FRAGMENT). [Source:SWISSPROT;Acc:Q9NU19]	0.0359807	0.132771	0.270998185	TBC1D22B	
560	ELAV-LIKE PROTEIN 3 (HU-ANTIGEN C) (HUC) (PARANEOPLASTIC CEREBELLAR DEGENERATION-ASSOCIATED ANTIGEN) (PARANEOPLASTIC LIMBIC ENCEPHALITIS ANTIGEN 21). [Source:SWISSPROT;Acc:Q14576]	0.539175	1.99055	0.270867348		
561	POLYPEPTIDE N-ACETYLGALACTOSAMINYLTRANSFERASE 2; UDP-GALNAC TRANSFERASE 2. [Source:RefSeq;Acc:NM_004481]	0.0483159	0.178411	0.270812338	GALNT2	
562		1.06428	3.92996	0.270811917	RAD54L2	
563		0.230346	0.850576	0.270811779	BTBD9	
564	SIMILAR TO EXPRESSED SEQUENCE AI415388 (FRAGMENT). [Source:SPTREMBL;Acc:Q8N428]	0.0370824	0.136931	0.270810846	GALNTL1	
565	"SERINE/THREONINE PROTEIN PHOSPHATASE 2A, 65 KDA REGULATORY SUBUNIT A, ALPHA ISOFORM (PP2A, SUBUNIT A, PR65-ALPHA ISOFORM) (PP2A, SUBUNIT A, R1-ALPHA ISOFORM) (MEDIUM TUMOR ANTIGEN-ASSOCIATED 61 KDA PROTEIN). [Source:SWISSPROT;Acc:P30153]"	0.1722	0.635895	0.270799424	PPP2R1A	
566	ELAV-LIKE PROTEIN 1 (HU-ANTIGEN R) (HUR). [Source:SWISSPROT;Acc:Q15717]	0.449826	1.66144	0.270744655	ELAVL1	
567		0.136702	0.504965	0.270715792	DHRS7B	
568	SIMILAR TO KINASE SUPPRESSOR OF RAS (FRAGMENT). [Source:SPTREMBL;Acc:Q8IVT5]	0.0932883	0.344638	0.270684893	KSR1	
569	DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 2 (EC 2.7.1.-) (MAP KINASE KINASE 2) (MAPKK 2) (ERK ACTIVATOR KINASE 2) (MAPK/ERK KINASE 2) (MEK2). [Source:SWISSPROT;Acc:P36507]	0.251342	0.928542	0.270684579	MAP2K2	
570	DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 1 (EC 2.7.1.-) (MAP KINASE KINASE 1) (MAPKK 1) (ERK ACTIVATOR KINASE 1) (MAPK/ERK KINASE 1) (MEK1). [Source:SWISSPROT;Acc:Q02750]	0.251342	0.928542	0.270684579	MAP2K1	
571		0.0726249	0.268301	0.270684418	KSR2	
572	ELAV-LIKE PROTEIN 4 (PARANEOPLASTIC ENCEPHALOMYELITIS ANTIGEN HUD) (HU-ANTIGEN D). [Source:SWISSPROT;Acc:P26378]	0.495507	1.83073	0.270660884	ELAVL4	
573	"SERINE/THREONINE PROTEIN PHOSPHATASE 2A, 65 KDA REGULATORY SUBUNIT A, BETA ISOFORM (PP2A, SUBUNIT A, PR65-BETA ISOFORM) (PP2A, SUBUNIT A, R1-BETA ISOFORM). [Source:SWISSPROT;Acc:P30154]"	0.181797	0.671805	0.270609775	PPP2R1B	
574	ELAV-LIKE PROTEIN 2 (HU-ANTIGEN B) (HUB) (ELAV-LIKE NEURONAL PROTEIN 1) (NERVOUS SYSTEM-SPECIFIC RNA BINDING PROTEIN HEL-N1). [Source:SWISSPROT;Acc:Q12926]	0.495602	1.83168	0.270572371	ELAVL2	
575	BILE ACID COENZYME A: AMINO ACID N-ACYLTRANSFERASE; GLYCINE N-CHOLOYLTRANSFERASE. [Source:RefSeq;Acc:NM_001701]	0.200205	0.740509	0.270361333	BAAT	
576	PEROXISOMAL ACYL-COENZYME A THIOESTER HYDROLASE 2A (EC 3.1.2.2) (PEROXISOMAL LONG-CHAIN ACYL-COA THIOESTERASE 2) (ZAP128). [Source:SWISSPROT;Acc:P49753]	0.230682	0.853273	0.270349583	ACOT1	
577	PEROXISOMAL ACYL-COA THIOESTERASE 2B; LIKELY ORTHOLOG OF MOUSE PEROXISOMAL ACYL-COA THIOESTERASE 2B. [Source:RefSeq;Acc:NM_152331]	0.257341	0.951909	0.270342018	ACOT4	
578		0.565201	2.09213	0.270155774	IRF2BP2	
579		0.483254	1.78896	0.270131249	C14orf4	
580	HEPATOCYTE NUCLEAR FACTOR 3-ALPHA (HNF-3A) (FORKHEAD BOX PROTEIN A1). [Source:SWISSPROT;Acc:P55317]	0.404388	1.49712	0.270110612	FOXA1	
581	UBIQUITIN-LIKE PROTEIN SUMO-1 CONJUGATING ENZYME (EC 6.3.2.19) (SUMO- 1-PROTEIN LIGASE) (UBIQUITIN CARRIER PROTEIN) (UBIQUITIN-CONJUGATING ENZYME UBCE2A) (P18). [Source:SWISSPROT;Acc:P50550]	0.334862	1.23982	0.270089206	UBE2I	
582	"SERINE/THREONINE PROTEIN PHOSPHATASE 2A, 55 KDA REGULATORY SUBUNIT B, ALPHA ISOFORM (PP2A, SUBUNIT B, B-ALPHA ISOFORM) (PP2A, SUBUNIT B, B55-ALPHA ISOFORM) (PP2A, SUBUNIT B, PR55-ALPHA ISOFORM) (PP2A, SUBUNIT B, R2-ALPHA ISOFORM). [Source:SWISSPROT;Acc:Q0"	0.0948257	0.351165	0.270031751		
583	UNCHARACTERIZED HEMATOPOIETIC STEM/PROGENITOR CELLS PROTEIN MDS026. [Source:SPTREMBL;Acc:Q9NZ48]	0.0951162	0.352242	0.270030831	PPP2R2D	
584	"SERINE/THREONINE PROTEIN PHOSPHATASE 2A, 55 KDA REGULATORY SUBUNIT B, BETA ISOFORM (PP2A, SUBUNIT B, B-BETA ISOFORM) (PP2A, SUBUNIT B, B55- BETA ISOFORM) (PP2A, SUBUNIT B, PR55-BETA ISOFORM) (PP2A, SUBUNIT B, R2-BETA ISOFORM). [Source:SWISSPROT;Acc:Q00005"	0.0961987	0.356254	0.270028407	PPP2R2B	
585	"SERINE/THREONINE PROTEIN PHOSPHATASE 2A, 55 KDA REGULATORY SUBUNIT B, GAMMA ISOFORM (PP2A, SUBUNIT B, B-GAMMA ISOFORM) (PP2A, SUBUNIT B, B55-GAMMA ISOFORM) (PP2A, SUBUNIT B, PR55-GAMMA ISOFORM) (PP2A, SUBUNIT B, R2-GAMMA ISOFORM) (IMYPNO1). [Source:SWISSP"	0.101295	0.375141	0.270018473	PPP2R2C	
586	CYCLIC-AMP-DEPENDENT TRANSCRIPTION FACTOR ATF-2 (ACTIVATING TRANSCRIPTION FACTOR 2) (CAMP RESPONSE ELEMENT BINDING PROTEIN CRE- BP1) (HB16). [Source:SWISSPROT;Acc:P15336]	0.673422	2.49889	0.269488453	ATF2	
587	CYCLIC-AMP-DEPENDENT TRANSCRIPTION FACTOR ATF-7 (ACTIVATING TRANSCRIPTION FACTOR 7) (TRANSCRIPTION FACTOR ATF-A). [Source:SWISSPROT;Acc:P17544]	0.574984	2.13394	0.269447126	ATF7	
588	40S RIBOSOMAL PROTEIN S8. [Source:SWISSPROT;Acc:P09058]	0.122515	0.454799	0.269382738	RPS8	
589		0.393043	1.45917	0.269360664	PGM2L1	
590	5'-METHYLTHIOADENOSINE PHOSPHORYLASE (EC 2.4.2.28) (MTA PHOSPHORYLASE) (MTAPASE). [Source:SWISSPROT;Acc:Q13126]	0.12174	0.452001	0.269335687	MTAP	
591	PUTATIVE RIBOSOMAL RNA METHYLTRANSFERASE 1 (EC 2.1.1.-) (RRNA (URIDINE-2'-O-)-METHYLTRANSFERASE) (JM23 PROTEIN). [Source:SWISSPROT;Acc:Q9UET6]	0.12174	0.452001	0.269335687	FTSJ1	
592	"SPECTRIN BETA CHAIN, BRAIN 2 (SPECTRIN, NON-ERYTHROID BETA CHAIN 2) (BETA-III SPECTRIN). [Source:SWISSPROT;Acc:O15020]"	0.0341846	0.126926	0.269327009	SPTBN2	
593		0.460943	1.71147	0.269325784	PGM2	
594	PHOSPHOACETYLGLUCOSAMINE MUTASE (EC 5.4.2.3) (PAGM) (ACETYLGLUCOSAMINE PHOSPHOMUTASE) (N-ACETYLGLUCOSAMINE-PHOSPHATE MUTASE) (PHOSPHOGLUCOMUTASE 3). [Source:SWISSPROT;Acc:O95394]	0.537765	1.99671	0.269325541	PGM3	
595	"SPECTRIN BETA CHAIN, BRAIN 1 (SPECTRIN, NON-ERYTHROID BETA CHAIN 1) (BETA-II SPECTRIN) (FODRIN BETA CHAIN). [Source:SWISSPROT;Acc:Q01082]"	0.0426374	0.158312	0.26932513	SPTBN1	
596	HEPATOCYTE NUCLEAR FACTOR 3-BETA (HNF-3B) (FORKHEAD BOX PROTEIN A2). [Source:SWISSPROT;Acc:Q9Y261]	0.414022	1.53743	0.269294862	FOXA2	
597	LIM DOMAIN ONLY 7; ZINC-FINGER DOMAIN-CONTAINING PROTEIN; LOMP PROTEIN; F-BOX ONLY PROTEIN 20; F-BOX PROTEIN FBX20. [Source:RefSeq;Acc:NM_005358]	0.126132	0.468539	0.269202777	LMO7	
598	CAMP RESPONSE ELEMENT-BINDING PROTEIN CRE-BPA. [Source:RefSeq;Acc:NM_004904]	0.132014	0.490424	0.2691834	CREB5	
599	ZINC FINGER PROTEIN ZIC 2 (ZINC FINGER PROTEIN OF THE CEREBELLUM 2). [Source:SWISSPROT;Acc:O95409]	0.307359	1.14212	0.269112703	ZIC2	
600	ZINC FINGER PROTEIN ZIC 3 (ZINC FINGER PROTEIN OF THE CEREBELLUM 3). [Source:SWISSPROT;Acc:O60481]	0.25098	0.932647	0.269105031	ZIC3	

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/