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 1252 to 1301 of 3206 in total

Rank	description	measured	expected	final	Hugo	
1252	METHYLENETETRAHYDROFOLATE REDUCTASE (EC 1.5.1.20). [Source:SWISSPROT;Acc:P42898]	0.121247	0.490121	0.247381769	MTHFR	
1253	IMPORTIN 4. [Source:RefSeq;Acc:NM_024658]	0.572386	2.31408	0.247349271		
1254	SERINE/THREONINE PROTEIN KINASE 13 (EC 2.7.1.37) (AURORA/IPL1/EG2 PROTEIN 2) (AURORA/IPL1-RELATED KINASE 3) (AURORA-C). [Source:SWISSPROT;Acc:Q9UQB9]	0.0283804	0.114745	0.247334524	AURKC	
1255	SERINE/THREONINE KINASE 6 (EC 2.7.1.37) (SERINE/THREONINE KINASE 15) (AURORA/IPL1-RELATED KINASE 1) (AURORA-RELATED KINASE 1) (HARK1) (AURORA-A) (BREAST-TUMOR-AMPLIFIED KINASE). [Source:SWISSPROT;Acc:O14965]	0.0366317	0.148106	0.247334342	AURKA	
1256	"CYLINDROMATOSIS (TURBAN TUMOR SYNDROME); CYLINDROMATOSIS 1, TURBAN TUMOR SYNDROME. [Source:RefSeq;Acc:NM_015247]"	0.0366317	0.148106	0.247334342	CYLD	
1257	SERINE/THREONINE PROTEIN KINASE 12 (EC 2.7.1.37) (AURORA- AND IPL1- LIKE MIDBODY-ASSOCIATED PROTEIN 1) (AIM-1) (AURORA/IPL1-RELATED KINASE 2) (AURORA-RELATED KINASE 2) (STK-1) (AURORA-B). [Source:SWISSPROT;Acc:Q96GD4]	0.0285544	0.115449	0.247333455	AURKB	
1258	KINESIN-LIKE PROTEIN KIF23 (MITOTIC KINESIN-LIKE PROTEIN-1) (KINESIN- LIKE PROTEIN 5). [Source:SWISSPROT;Acc:Q02241]	0.310673	1.25609	0.247333392	KIF23	
1259		0.0339667	0.137332	0.247332741	AQR	
1260	ISCHEMIA/REPERFUSION INDUCIBLE PROTEIN. [Source:RefSeq;Acc:NM_024640]	0.0999509	0.404396	0.247160951		
1261		0.12467	0.504447	0.24714192		
1262		0.0311675	0.126112	0.24714143	SHQ1	
1263		0.110103	0.445662	0.247054943	C9orf7	
1264	LAMIN B2. [Source:SWISSPROT;Acc:Q03252]	0.481793	1.95026	0.247040395		
1265	BLOCK OF PROLIFERATION 1. [Source:SWISSPROT;Acc:Q14137]	0.872123	3.53236	0.246895277	BOP1	
1266	U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM8. [Source:SWISSPROT;Acc:O95777]	0.115741	0.46893	0.246819355	LSM8	
1267	NUCLEOLAR RNA-ASSOCIATED PROTEIN ALPHA ISOFORM. [Source:RefSeq;Acc:NM_022917]	0.966893	3.91912	0.246711762	NOL6	
1268	SINGLE-MINDED HOMOLOG 1. [Source:SWISSPROT;Acc:P81133]	0.0318532	0.12912	0.246694548	SIM1	
1269	PERIPHERAL PLASMA MEMBRANE PROTEIN CASK (EC 2.7.1.-) (HCASK) (CALCIUM/CALMODULIN-DEPENDENT SERINE PROTEIN KINASE) (LIN-2 HOMOLOG). [Source:SWISSPROT;Acc:O14936]	0.685788	2.77992	0.24669343	CASK	
1270	HYPOXIA-INDUCIBLE FACTOR-3 ALPHA ISOFORM A; INHIBITORY PAS DOMAIN PROTEIN. [Source:RefSeq;Acc:NM_152794]	0.0415296	0.168345	0.246693397	HIF3A	
1271		0.264834	1.07406	0.246572817		
1272	I-KAPPA-B-INTERACTING RAS-LIKE PROTEIN 2. [Source:RefSeq;Acc:NM_017595]	0.0342893	0.139064	0.246572082	NKIRAS2	
1273	KAPPA B-RAS 1. [Source:RefSeq;Acc:NM_020345]	0.0384625	0.155989	0.246571874		
1274	SNARE ASSOCIATED PROTEIN SNAPIN. [Source:RefSeq;Acc:NM_012437]	0.0384625	0.155989	0.246571874	SNAPAP	
1275	PROTEASOME SUBUNIT BETA TYPE 9 PRECURSOR (EC 3.4.25.1) (PROTEASOME CHAIN 7) (MACROPAIN CHAIN 7) (MULTICATALYTIC ENDOPEPTIDASE COMPLEX CHAIN 7) (RING12 PROTEIN) (LOW MOLECULAR MASS PROTEIN 2). [Source:SWISSPROT;Acc:P28065]	0.122196	0.495798	0.246463277		
1276	"MAGUK P55 SUBFAMILY MEMBER 2 (MPP2 PROTEIN) (DISCS, LARGE HOMOLOG 2). [Source:SWISSPROT;Acc:Q14168]"	0.123807	0.50235	0.246455658	MPP2	
1277	MAGUK P55 SUBFAMILY MEMBER 6 (VELI-ASSOCIATED MAGUK 1) (VAM-1). [Source:SWISSPROT;Acc:Q9NZW5]	0.143838	0.583751	0.246403004	MPP6	
1278	MYB PROTO-ONCOGENE PROTEIN (C-MYB). [Source:SWISSPROT;Acc:P10242]	0.139096	0.564523	0.24639563	MYB	
1279	EPSIN 1; EH DOMAIN-BINDING MITOTIC PHOSPHOPROTEIN. [Source:RefSeq;Acc:NM_013333]	0.0423484	0.171872	0.246394992	EPN1	
1280	CALRETICULIN PRECURSOR (CRP55) (CALREGULIN) (HACBP) (ERP60). [Source:SWISSPROT;Acc:P27797]	0.205692	0.834998	0.246338315	CALR	
1281	CATHEPSIN B PRECURSOR (EC 3.4.22.1) (CATHEPSIN B1) (APP SECRETASE). [Source:SWISSPROT;Acc:P07858]	0.264212	1.07259	0.246330844	CTSB	
1282	CYSTEINE-RICH MOTOR NEURON 1; CYSTEINE-RICH REPEAT-CONTAINING PROTEIN S52 PRECURSOR. [Source:RefSeq;Acc:NM_016441]	0.516861	2.10021	0.246099676	CRIM1	
1283	"NUCLEOSTEMIN; PUTATIVE NUCLEOTIDE BINDING PROTEIN, ESTRADIOL-INDUCED. [Source:RefSeq;Acc:NM_014366]"	0.856366	3.47989	0.246089963	GNL3	
1284		0.661293	2.68731	0.246079909	GNL3L	
1285		0.0982055	0.399189	0.24601254	GPR158	
1286		0.0245797	0.0999171	0.246000935	ISCA1	
1287	GUANINE NUCLEOTIDE-BINDING PROTEIN-LIKE 1 (GTP-BINDING PROTEIN HSR1). [Source:SWISSPROT;Acc:P36915]	0.129655	0.527051	0.246000861		
1288	ZINC FINGER-LIKE PROTEIN 9. [Source:RefSeq;Acc:NM_033414]	0.0473076	0.192307	0.246000406	ZNF622	
1289	MEMBRANE-ASSOCIATED TRANSPORTER PROTEIN (AIM-1 PROTEIN) (MELANOMA ANTIGEN AIM1). [Source:SWISSPROT;Acc:Q9UMX9]	0.0493513	0.200615	0.24600005	SLC45A2	
1290	60S RIBOSOMAL PROTEIN L19. [Source:SWISSPROT;Acc:P14118]	0.864722	3.51639	0.245911858	RPL19	
1291	N-TERMINAL ACETYLTRANSFERASE COMPLEX ARD1 SUBUNIT HOMOLOG (EC 2.3.1.-). [Source:SWISSPROT;Acc:P41227]	0.304267	1.23733	0.245906104	ARD1A	
1292	ECOTROPIC VIRAL INTEGRATION SITE 5; NEUROBLASTOMA STAGE 4S GENE. [Source:RefSeq;Acc:NM_005665]	0.0317084	0.128948	0.245900673	EVI5	
1293		0.111932	0.455193	0.245900091	C22orf23	
1294		0.160447	0.65249	0.245899554	RBMX2	
1295		0.0401118	0.163123	0.245899107	BUD13	
1296	SIMILAR TO ECOTROPIC VIRAL INTEGRATION SITE 5; NEUROBLASTOMA STAGE 4S GENE. [Source:RefSeq;Acc:NM_145245]	0.0401118	0.163123	0.245899107	EVI5L	
1297		0.108852	0.442722	0.245869869	UPRT	
1298		0.0760628	0.309407	0.245834128		
1299	DELTA-AMINOLEVULINIC ACID DEHYDRATASE (EC 4.2.1.24) (PORPHOBILINOGEN SYNTHASE) (ALADH). [Source:SWISSPROT;Acc:P13716]	0.154288	0.627636	0.245824013	ALAD	
1300	BAG-FAMILY MOLECULAR CHAPERONE REGULATOR-3 (BCL-2 BINDING ATHANOGENE- 3) (BAG-3) (BCL-2-BINDING PROTEIN BIS) (DOCKING PROTEIN CAIR-1). [Source:SWISSPROT;Acc:O95817]	0.0975531	0.396904	0.245785127	BAG3	
1301	RAC GTPASE ACTIVATING PROTEIN 1; GTPASE ACTIVATING PROTEIN. [Source:RefSeq;Acc:NM_013277]	0.268542	1.09266	0.245769041	RACGAP1	

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/