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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Gene Rank description measured expected final Hugo

Results: HTML CSV LaTeX

Showing element 1702 to 1751 of 3206 in total

Rank	description	measured	expected	final	Hugo	
1702	ELKS PROTEIN. [Source:RefSeq;Acc:NM_015064]	0.0412444	0.173407	0.237847376	ERC1	
1703	26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 3 (26S PROTEASOME REGULATORY SUBUNIT S3) (PROTEASOME SUBUNIT P58). [Source:SWISSPROT;Acc:O43242]	0.779642	3.27908	0.237762421	PSMD3	
1704	DJ408B20.3 (NOVEL PROTEIN SIMILAR TO 60S ACIDIC RIBOSOMAL PROTEIN P2 (RPLP2)). [Source:SPTREMBL;Acc:Q9H5A9]	0.0573148	0.241075	0.237746759		
1705	BETA-CENTRACTIN (ACTIN-RELATED PROTEIN 1B) (ARP1B). [Source:SWISSPROT;Acc:P42025]	0.0916612	0.385556	0.237737709	ACTR1B	
1706	ALPHA-CENTRACTIN (CENTRACTIN) (CENTROSOME-ASSOCIATED ACTIN HOMOLOG) (ACTIN-RPV) (ARP1). [Source:SWISSPROT;Acc:P42024]	0.0967911	0.407134	0.237737698	ACTR1A	
1707	26S PROTEASE REGULATORY SUBUNIT 6B (MIP224) (MB67 INTERACTING PROTEIN) (TAT-BINDING PROTEIN-7) (TBP-7). [Source:SWISSPROT;Acc:P43686]	0.848985	3.57194	0.237681764	PSMC4	
1708	VESICLE-FUSING ATPASE (EC 3.6.4.6) (VESICULAR-FUSION PROTEIN NSF) (N- ETHYLMALEIMIDE SENSITIVE FUSION PROTEIN) (NEM-SENSITIVE FUSION PROTEIN). [Source:SWISSPROT;Acc:P46459]	0.15883	0.66831	0.23765917	NSF	
1709	26S PROTEASE REGULATORY SUBUNIT 7 (MSS1 PROTEIN). [Source:SWISSPROT;Acc:P35998]	0.933253	3.92714	0.237641897	PSMC2	
1710	60S RIBOSOMAL PROTEIN L4 (L1). [Source:SWISSPROT;Acc:P36578]	0.83123	3.49797	0.237632112	RPL4	
1711		0.18248	0.768033	0.237593958	PNPLA7	
1712	26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 11 (26S PROTEASOME REGULATORY SUBUNIT S9) (26S PROTEASOME REGULATORY SUBUNIT P44.5). [Source:SWISSPROT;Acc:O00231]	0.667497	2.81169	0.237400638	PSMD11	
1713	26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 6 (26S PROTEASOME REGULATORY SUBUNIT S10) (P42A) (PROTEASOME REGULATORY PARTICLE SUBUNIT P44S10). [Source:SWISSPROT;Acc:Q15008]	0.750885	3.16322	0.237379948	PSMD6	
1714	"NUCLEOLAR PROTEIN FAMILY A, MEMBER 2; COMPONENT OF THE H/ACA SNORNP. [Source:RefSeq;Acc:NM_017838]"	0.0909039	0.382985	0.237356293	NOLA2	
1715	"TRANSCRIPTION INITIATION FACTOR IIF, ALPHA SUBUNIT (TFIIF-ALPHA) (TRANSCRIPTION INITIATION FACTOR RAP74). [Source:SWISSPROT;Acc:P35269]"	0.0303013	0.127662	0.237355674	GTF2F1	
1716	VACUOLAR PROTON TRANSLOCATING ATPASE 116 KDA SUBUNIT A ISOFORM 1 (CLATHRIN-COATED VESICLE/SYNAPTIC VESICLE PROTON PUMP 116 KDA SUBUNIT) (VACUOLAR PROTON PUMP SUBUNIT 1) (VACUOLAR ADENOSINE TRIPHOSPHATASE SUBUNIT AC116). [Source:SWISSPROT;Acc:Q93050]	0.269961	1.13756	0.237315834	ATP6V0A1	
1717	"ATPASE, H+ TRANSPORTING, LYSOSOMAL V0 SUBUNIT A ISOFORM 4; VACUOLAR PROTON PUMP 116 KDA ACCESSORY SUBUNIT; VACUOLAR PROTON PUMP, SUBUNIT 2; H(+)-TRANSPORTING TWO-SECTOR ATPASE, NONCATALYTIC ACCESSORY PROTEIN 1B; ATPASE, H+ TRANSPORTING, LYSOSOMAL (VACUOLA"	0.224133	0.944489	0.237306099	ATP6V0A4	
1718	VACUOLAR PROTON TRANSLOCATING ATPASE 116 KDA SUBUNIT A ISOFORM 2 (V-ATPASE 116-KDA ISOFORM A2) (TJ6). [Source:SWISSPROT;Acc:Q9Y487]	0.211834	0.892673	0.237303021	ATP6V0A2	
1719	VACUOLAR PROTON TRANSLOCATING ATPASE 116 KDA SUBUNIT A ISOFORM 3 (V- ATPASE 116-KDA ISOFORM A3) (OSTEOCLASTIC PROTON PUMP 116 KDA SUBUNIT) (OC-116 KDA) (OC116) (T-CELL IMMUNE REGULATOR 1) (T CELL IMMUNE RESPONSE CDNA7 PROTEIN) (TIRC7). [Source:SWISSPROT;A	0.202198	0.852079	0.237299593	TCIRG1	
1720	MIDASIN (MIDAS-CONTAINING PROTEIN). [Source:SWISSPROT;Acc:Q9NU22]	0.321031	1.35288	0.237294512	MDN1	
1721	26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 9 (26S PROTEASOME REGULATORY SUBUNIT P27). [Source:SWISSPROT;Acc:O00233]	0.154828	0.652697	0.237212673	PSMD9	
1722	"PROBABLE DIMETHYLADENOSINE TRANSFERASE (EC 2.1.1.-) (S- ADENOSYLMETHIONINE-6-N',N'-ADENOSYL(RRNA) DIMETHYLTRANSFERASE) (18S RRNA DIMETHYLASE). [Source:SWISSPROT;Acc:Q9UNQ2]"	0.367472	1.54946	0.237161334	DIMT1L	
1723	VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 45 (H-VPS45) (HLVPS45). [Source:SWISSPROT;Acc:Q9NRW7]	0.230384	0.971531	0.237134996	VPS45	
1724		0.0547796	0.231086	0.237052872	RIOK2	
1725		0.10685	0.450769	0.23703937	VPS25	
1726		0.10685	0.450769	0.23703937	CHMP6	
1727	"GLUTAMATE DECARBOXYLASE, 65 KDA ISOFORM (EC 4.1.1.15) (GAD-65) (65 KDA GLUTAMIC ACID DECARBOXYLASE). [Source:SWISSPROT;Acc:Q05329]"	0.0175982	0.0742417	0.237039292	GAD2	
1728		0.0787698	0.332307	0.237039244	C12orf26	
1729	"GAMMA-SOLUBLE NSF ATTACHMENT PROTEIN (SNAP-GAMMA) (N-ETHYLMALEIMIDE- SENSITIVE FACTOR ATTACHMENT PROTEIN, GAMMA). [Source:SWISSPROT;Acc:Q99747]"	0.056545	0.238547	0.237039242	NAPG	
1730	NOSTRIN. [Source:RefSeq;Acc:NM_052946]	0.02137	0.0901539	0.237039108	NOSTRIN	
1731		0.02137	0.0901539	0.237039108		
1732	"GLUTAMATE DECARBOXYLASE, 67 KDA ISOFORM (EC 4.1.1.15) (GAD-67) (67 KDA GLUTAMIC ACID DECARBOXYLASE). [Source:SWISSPROT;Acc:Q99259]"	0.0213112	0.0899059	0.237038949	GAD1	
1733	"LIV-1 PROTEIN, ESTROGEN REGULATED. [Source:RefSeq;Acc:NM_012319]"	0.0166846	0.0703876	0.23703891	SLC39A6	
1734	EAP30 SUBUNIT OF ELL COMPLEX. [Source:RefSeq;Acc:NM_007241]	0.04274	0.180308	0.237038845	SNF8	
1735	RAD54-LIKE PROTEIN; RAD54 HOMOLOG. [Source:RefSeq;Acc:NM_003579]	0.180241	0.760447	0.237019805	RAD54L	
1736		0.630807	2.66198	0.236969098	ATPBD3	
1737	GLUTAMINYL-TRNA SYNTHASE (GLUTAMINE-HYDROLYZING)-LIKE 1. [Source:RefSeq;Acc:NM_018292]	0.094576	0.399107	0.236969033	QRSL1	
1738	FATTY-ACID AMIDE HYDROLASE (EC 3.1.-.-) (OLEAMIDE HYDROLASE) (ANANDAMIDE AMIDOHYDROLASE). [Source:SWISSPROT;Acc:O00519]	0.0947181	0.399707	0.23696883	FAAH	
1739	"URACIL-DNA GLYCOSYLASE, MITOCHONDRIAL PRECURSOR (EC 3.2.2.-) (UDG). [Source:SWISSPROT;Acc:P13051]"	0.0946707	0.399507	0.236968814	UNG	
1740	"PROBABLE GLUTAMYL-TRNA(GLN) AMIDOTRANSFERASE SUBUNIT B, MITOCHONDRIAL PRECURSOR (EC 6.3.5.-) (GLU-ADT SUBUNIT B) (CYTOCHROME OXIDASE ASSEMBLY FACTOR PET112 HOMOLOG). [Source:SWISSPROT;Acc:O75879]"	0.0946707	0.399507	0.236968814	PET112L	
1741	COACTOSIN-LIKE PROTEIN. [Source:SWISSPROT;Acc:Q14019]	0.0315727	0.133236	0.236968237	COTL1	
1742	CONSERVED OLIGOMERIC GOLGI COMPLEX COMPONENT 6. [Source:SWISSPROT;Acc:Q9Y2V7]	0.0676104	0.2855	0.236814011	COG6	
1743	40S RIBOSOMAL PROTEIN S28. [Source:SWISSPROT;Acc:P25112]	0.229236	0.968071	0.236796681		
1744	"VACUOLAR ATP SYNTHASE SUBUNIT B, BRAIN ISOFORM (EC 3.6.3.14) (V-ATPASE B2 SUBUNIT) (VACUOLAR PROTON PUMP B ISOFORM 2) (ENDOMEMBRANE PROTON PUMP 58 KDA SUBUNIT) (HO57). [Source:SWISSPROT;Acc:P21281]"	0.357744	1.51127	0.236717463	ATP6V1B2	
1745	GANGLIOSIDE-INDUCED DIFFERENTIATION-ASSOCIATED PROTEIN 1-LIKE 1. [Source:RefSeq;Acc:NM_024034]	0.0826697	0.349234	0.236717215	GDAP1L1	
1746	YEAST SEC31P HOMOLOG. [Source:RefSeq;Acc:NM_014933]	0.134029	0.566199	0.236717126	SEC31A	
1747	VACUOLAR ATP SYNTHASE SUBUNIT E (EC 3.6.3.14) (V-ATPASE E SUBUNIT) (VACUOLAR PROTON PUMP E SUBUNIT) (V-ATPASE 31 KDA SUBUNIT) (P31). [Source:SWISSPROT;Acc:P36543]	0.480242	2.02876	0.236717009	ATP6V1E1	
1748	GANGLIOSIDE-INDUCED DIFFERENTIATION-ASSOCIATED PROTEIN 1. [Source:RefSeq;Acc:NM_018972]	0.0973611	0.411298	0.236716687	GDAP1	
1749	VACUOLAR ATP SYNTHASE SUBUNIT D (EC 3.6.3.14) (V-ATPASE D SUBUNIT) (VACUOLAR PROTON PUMP D SUBUNIT) (V-ATPASE 28 KDA ACCESSORY PROTEIN). [Source:SWISSPROT;Acc:Q9Y5K8]	0.518099	2.18869	0.236716483	ATP6V1D	
1750	VACUOLAR ATP SYNTHASE SUBUNIT H (EC 3.6.3.14) (V-ATPASE H SUBUNIT) (VACUOLAR PROTON PUMP H SUBUNIT) (V-ATPASE 50/57 KDA SUBUNITS) (VACUOLAR PROTON PUMP SUBUNIT SFD) (CGI-11). [Source:SWISSPROT;Acc:Q9UI12]	0.0562476	0.237616	0.236716383	ATP6V1H	
1751	VACUOLAR ATP SYNTHASE SUBUNIT G 2 (EC 3.6.3.14) (V-ATPASE G SUBUNIT 2) (VACUOLAR PROTON PUMP G SUBUNIT 2) (V-ATPASE 13 KDA SUBUNIT 2). [Source:SWISSPROT;Acc:O95670]	0.0861167	0.363797	0.236716356		

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/