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 952 to 1001 of 3206 in total

Rank	description	measured	expected	final	Hugo	
952	SIMILAR TO PUTATIVE TRANSMEMBRANE PROTEIN; HOMOLOG OF YEAST GOLGI MEMBRANE PROTEIN YIF1P (YIP1P-INTERACTING FACTOR). [Source:RefSeq;Acc:NM_033557]	0.135079	0.526818	0.256405438	YIF1B	
953	ALPHA/BETA HYDROLASE DOMAIN CONTAINING PROTEIN 1 ISOFORM 2; LUNG ALPHA/BETA HYDROLASE PROTEIN 1. [Source:RefSeq;Acc:NM_152870]	0.0261125	0.101841	0.256404591	ABHD1	
954	IMPORTIN ALPHA-1 SUBUNIT (KARYOPHERIN ALPHA-1 SUBUNIT) (SRP1-BETA) (RAG COHORT PROTEIN 2) (NUCLEOPROTEIN INTERACTOR 1) (NPI-1). [Source:SWISSPROT;Acc:P52294]	1.24311	4.84902	0.256363141	KPNA1	
955	VACUOLAR PROTEIN SORTING 16 (HVPS16). [Source:SWISSPROT;Acc:Q9H269]	0.209882	0.818777	0.256335974	PTPRA	
956	60S RIBOSOMAL PROTEIN L24 (L30). [Source:SWISSPROT;Acc:P38663]	0.308685	1.20423	0.256333923	RPL24	
957	CTP SYNTHASE (EC 6.3.4.2) (UTP--AMMONIA LIGASE) (CTP SYNTHETASE). [Source:SWISSPROT;Acc:P17812]	0.288835	1.12692	0.256304795	CTPS	
958		0.0783783	0.305823	0.256286479	TIMM50	
959	CYTIDINE TRIPHOSPHATE SYNTHASE II; CTP SYNTHETASE TYPE 2; UTP-AMMONIA LIGASE; CTP SYNTHETASE ISOFORM; CYTIDINE 5'-TRIPHOSPHATE SYNTHETASE 2. [Source:RefSeq;Acc:NM_019857]	0.226073	0.882186	0.256264552	CTPS2	
960	"ACYL-COA DEHYDROGENASE, SHORT/BRANCHED CHAIN SPECIFIC, MITOCHONDRIAL PRECURSOR (EC 1.3.99.-) (SBCAD) (2-METHYL BRANCHED CHAIN ACYL-COA DEHYDROGENASE) (2-MEBCAD) (2-METHYLBUTYRYL-COENZYME A DEHYDROGENASE) (2-METHYLBUTYRYL-COA DEHYDROGENASE). [Source:SWISSP"	0.0614814	0.240043	0.256126611		
961	PDZ/COILED-COIL DOMAIN BINDING PARTNER FOR THE RHO-FAMILY GTPASE TC10; FUSED IN GLIOBLASTOMA; GOLGI ASSOCIATED PDZ AND COILED-COIL MOTIF CONTAINING PROTEIN; CFTR-ASSOCIATED LIGAND. [Source:RefSeq;Acc:NM_020399]	0.909945	3.55389	0.256041971	GOPC	
962	PRIP-INTERACTING PROTEIN PIPMT; PRIP-INTERACTING PROTEIN WITH METHYLTRANSFERASE DOMAIN. [Source:RefSeq;Acc:NM_024831]	0.0391646	0.152962	0.25604137	TGS1	
963		0.0391646	0.152962	0.25604137	C6orf32	
964	STRUCTURE-SPECIFIC RECOGNITION PROTEIN 1 (SSRP1) (RECOMBINATION SIGNAL SEQUENCE RECOGNITION PROTEIN) (T160) (CHROMATIN-SPECIFIC TRANSCRIPTION ELONGATION FACTOR 80 KDA SUBUNIT) (FACT 80 KDA SUBUNIT). [Source:SWISSPROT;Acc:Q08945]	0.031735	0.124	0.255927419	SSRP1	
965	CHROMATIN-SPECIFIC TRANSCRIPTION ELONGATION FACTOR LARGE SUBUNIT. [Source:RefSeq;Acc:NM_007192]	0.12694	0.496001	0.255926903	SUPT16H	
966	PROTEIN TRANSLATION FACTOR SUI1 HOMOLOG GC20. [Source:SWISSPROT;Acc:O60739]	0.553061	2.16185	0.255827648	EIF1B	
967	EUKARYOTIC PEPTIDE CHAIN RELEASE FACTOR SUBUNIT 1 (ERF1) (EUKARYOTIC RELEASE FACTOR 1) (TB3-1) (C11 PROTEIN). [Source:SWISSPROT;Acc:P46055]	0.100509	0.39329	0.255559511	ETF1	
968	DNAJ HOMOLOG SUBFAMILY B MEMBER 5 (HEAT SHOCK PROTEIN HSP40-3) (HEAT SHOCK PROTEIN COGNATE 40) (HSC40) (HSP40-2). [Source:SWISSPROT;Acc:O75953]	0.0721855	0.282461	0.255559175	DNAJB5	
969	DNAJ HOMOLOG SUBFAMILY B MEMBER 4 (HEAT SHOCK 40 KDA PROTEIN 1 HOMOLOG) (HEAT SHOCK PROTEIN 40 HOMOLOG) (HSP40 HOMOLOG). [Source:SWISSPROT;Acc:Q9UDY4]	0.0721855	0.282461	0.255559175	DNAJB4	
970	CAB2. [Source:RefSeq;Acc:NM_033419]	0.0366052	0.143236	0.255558658	PERLD1	
971	SUPPRESSOR OF ACTIN MUTATIONS 2-LIKE ISOFORM B; DJ1033B10.5. [Source:RefSeq;Acc:NM_022553]	0.281375	1.10102	0.255558482	VPS52	
972	DNAJ HOMOLOG SUBFAMILY B MEMBER 1 (HEAT SHOCK 40 KDA PROTEIN 1) (HEAT SHOCK PROTEIN 40) (HSP40) (DNAJ PROTEIN HOMOLOG 1) (HDJ-1). [Source:SWISSPROT;Acc:P25685]	0.0597214	0.23369	0.255558218	DNAJB1	
973	G1 TO S PHASE TRANSITION PROTEIN 1 HOMOLOG (GTP-BINDING PROTEIN GST1-HS). [Source:SWISSPROT;Acc:P15170]	0.117727	0.460892	0.255432943	GSPT1	
974	TRANSDUCIN-LIKE ENHANCER PROTEIN 4. [Source:SWISSPROT;Acc:Q04727]	0.354858	1.38936	0.255411125	TLE4	
975	SON PROTEIN (SON3) (NEGATIVE REGULATORY ELEMENT-BINDING PROTEIN) (NRE- BINDING PROTEIN) (DBP-5) (BAX ANTAGONIST SELECTED IN SACCHAROMYCES 1) (BASS1) (PROTEIN C21ORF50). [Source:SWISSPROT;Acc:P18583]	0.095104	0.372361	0.255408058	SON	
976	60S ACIDIC RIBOSOMAL PROTEIN P2. [Source:SWISSPROT;Acc:P05387]	0.114475	0.44823	0.255393436	RPLP2	
977	TSC22-RELATED INDUCIBLE LEUCINE ZIPPER PROTEIN 2 (TSC-22-LIKE PROTEIN THG-1). [Source:SWISSPROT;Acc:Q9Y3Q8]	0.149858	0.586856	0.255357362	TSC22D4	
978	SPHINGOLIPID DELTA 4 DESATURASE; MEMBRANE FATTY ACID (LIPID) DESATURASE; DIHYDROCERAMIDE DESATURASE. [Source:RefSeq;Acc:NM_003676]	0.0374644	0.146714	0.25535668	DEGS1	
979	"FRUCTOSE-1,6-BISPHOSPHATASE (EC 3.1.3.11) (D-FRUCTOSE-1,6-BISPHOSPHATE 1-PHOSPHOHYDROLASE) (FBPASE). [Source:SWISSPROT;Acc:P09467]"	0.136601	0.535042	0.255308929	FBP1	
980		0.32192	1.26105	0.255279331		
981	60 KDA TAT INTERACTIVE PROTEIN (TIP60) (HIV-1 TAT INTERACTIVE PROTEIN) (CPLA(2) INTERACTING PROTEIN). [Source:SWISSPROT;Acc:Q92993]	0.0395897	0.155084	0.255279075	HTATIP	
982	SORTING NEXIN 6 (TRAF4-ASSOCIATED FACTOR 2). [Source:SWISSPROT;Acc:Q9UNH7]	0.314547	1.23231	0.255249897	SNX6	
983	"FRUCTOSE-1,6-BISPHOSPHATASE ISOZYME 2 (EC 3.1.3.11) (D-FRUCTOSE-1,6- BISPHOSPHATE 1-PHOSPHOHYDROLASE) (FBPASE). [Source:SWISSPROT;Acc:O00757]"	0.12174	0.47704	0.255198725	FBP2	
984	TRANSDUCIN-LIKE ENHANCER PROTEIN 3 (ESG3). [Source:SWISSPROT;Acc:Q04726]	0.333664	1.30756	0.255180642	TLE3	
985	CYTOKINE-LIKE NUCLEAR FACTOR N-PAC. [Source:RefSeq;Acc:NM_032569]	0.11603	0.454719	0.255168577		
986		0.087747	0.343879	0.255168242	HECW2	
987	ACTIVATOR OF BASAL TRANSCRIPTION 1; TATA-BINDING PROTEIN-BINDING PROTEIN; BASAL TRANSCRIPTIONAL ACTIVATOR. [Source:RefSeq;Acc:NM_013375]	0.0349473	0.136958	0.255168008	ABT1	
988	HECT TYPE E3 UBIQUITIN LIGASE. [Source:RefSeq;Acc:NM_015052]	0.0745937	0.292332	0.255167754	HECW1	
989	CPG BINDING PROTEIN (PROTEIN CONTAINING PHD FINGER AND CXXC DOMAIN 1). [Source:SWISSPROT;Acc:Q9P0U4]	0.0439174	0.172112	0.255167565	CXXC1	
990	HOMEOBOX PROTEIN ENGRAILED-2 (HU-EN-2). [Source:SWISSPROT;Acc:P19622]	0.283289	1.11021	0.25516704	EN2	
991	"ALPHA-(1,6)-FUCOSYLTRANSFERASE (EC 2.4.1.68) (GLYCOPROTEIN 6-ALPHA-L- FUCOSYLTRANSFERASE) (GDP-FUCOSE--GLYCOPROTEIN FUCOSYLTRANSFERASE) (GDP-L-FUC:N-ACETYL-BETA-D-GLUCOSAMINIDE ALPHA1,6-FUCOSYLTRANSFERASE) (ALPHA1-6FUCT) (FUCOSYLTRANSFERASE 8). [Source:SW"	0.0378287	0.148317	0.255053028	FUT8	
992	INOSITOL POLYPHOSPHATE MULTIKINASE. [Source:RefSeq;Acc:NM_152230]	0.0744186	0.291777	0.255053003	IPMK	
993	AFG3-LIKE PROTEIN 2 (EC 3.4.24.-) (PARAPLEGIN-LIKE PROTEIN). [Source:SWISSPROT;Acc:Q9Y4W6]	0.282136	1.10619	0.255052025	AFG3L2	
994	PROTEASOME SUBUNIT BETA TYPE 4 PRECURSOR (EC 3.4.25.1) (PROTEASOME BETA CHAIN) (MACROPAIN BETA CHAIN) (MULTICATALYTIC ENDOPEPTIDASE COMPLEX BETA CHAIN) (PROTEASOME CHAIN 3) (HSN3) (HSBPROS26). [Source:SWISSPROT;Acc:P28070]	0.753893	2.95595	0.255042541	PSMB4	
995	TRANSDUCIN-LIKE ENHANCER PROTEIN 1 (ESG1). [Source:SWISSPROT;Acc:Q04724]	0.357881	1.40331	0.255026331		
996	TRANSDUCIN-LIKE ENHANCER PROTEIN 2 (ESG2). [Source:SWISSPROT;Acc:Q04725]	0.304091	1.19246	0.255011489	TLE2	
997	RIBONUCLEOTIDE REDUCTASE M2 B (TP53 INDUCIBLE); P53-INDUCIBLE RIBONUCLEOTIDE REDUCTASE SMALL SUBUNIT 2 HOMOLOG. [Source:RefSeq;Acc:NM_015713]	0.226174	0.88694	0.255004848	RRM2B	
998		0.115392	0.452671	0.254913613	NUAK2	
999	"N-ACETYLLACTOSAMINIDE BETA-1,3-N-ACETYLGLUCOSAMINYLTRANSFERASE (EC 2.4.1.149) (POLY-N-ACETYLLACTOSAMINE EXTENSION ENZYME) (I-BETA- 1,3-N-ACETYLGLUCOSAMINYLTRANSFERASE) (IGNT) (UDP-GLCNAC:BETAGAL BETA- 1,3-N-ACETYLGLUCOSAMINYLTRANSFERASE 6). [Source:SWISSP"	0.036112	0.141665	0.254911234	B3GNT1	
1000		0.143571	0.56322	0.254911047	ISOC2	
1001	MITOCHONDRIAL IMPORT INNER MEMBRANE TRANSLOCASE SUBUNIT TIM10. [Source:SWISSPROT;Acc:Q9Y5J8]	0.0670247	0.262934	0.254910738	TIMM10	

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/