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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expected measured Gene Hugo final Rank description

Results: HTML CSV LaTeX

Showing element 101 to 150 of 3206 in total

expected	measured	Hugo	final	Rank	description
0.104721	0.00386024	CHMP2B	0.036862138	3199
0.104827	0.0215242	VAMP3	0.205330688	2735	VESICLE-ASSOCIATED MEMBRANE PROTEIN 3 (VAMP-3) (SYNAPTOBREVIN 3) (CELLUBREVIN) (CEB). [SWISSPROT;Acc:Q15836]
0.104865	0.0223249	SLC25A13	0.212891813	2589	"CALCIUM-BINDING MITOCHONDRIAL CARRIER PROTEIN ARALAR2 (SOLUTE CARRIER FAMILY 25, MEMBER 13) (CITRIN). [SWISSPROT;Acc:Q9UJS0]"
0.104981	0.0243256	FAM98B	0.23171431	1931
0.105024	0.0255702	COQ2	0.243470064	1443
0.105517	0.024834	no value	0.23535544	1782	17 BETA-HYDROXYSTEROID DEHYDROGENASE. [SPTREMBL;Acc:Q13034]
0.105559	0.0256005	NGDN	0.242523139	1511
0.105652	0.0256013	NET1	0.24231723	1528	NEUROEPITHELIAL CELL TRANSFORMING GENE 1; GUANINE NUCLEOTIDE REGULATORY PROTEIN (ONCOGENE); RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR (GEF) 8. [RefSeq;Acc:NM_005863]
0.106604	0.0260119	HS6ST2	0.244004915	1410	HEPARAN SULFATE 6-O-SULFOTRANSFERASE 2. [RefSeq;Acc:NM_147174]
0.106609	0.0275088	SLC37A1	0.2580345	913	GLYCEROL-3-PHOSPHATE TRANSPORTER (G-3-P TRANSPORTER) (G-3-P PERMEASE). [SWISSPROT;Acc:P57057]
0.106724	0.0240186	NUCB1	0.225053409	2212	NUCLEOBINDIN 1 PRECURSOR (CALNUC). [SWISSPROT;Acc:Q02818]
0.106766	0.0285187	no value	0.267114063	659	SECRETED MODULAR CALCIUM-BINDING PROTEIN 1. [RefSeq;Acc:NM_022137]
0.106779	0.0243642	DPY19L2P2	0.228174079	2116
0.10746	0.0270059	PGAM2	0.251311186	1096	PHOSPHOGLYCERATE MUTASE 2 (EC 5.4.2.1) (EC 5.4.2.4) (EC 3.1.3.13) (PHOSPHOGLYCERATE MUTASE ISOZYME M) (PGAM-M) (BPG-DEPENDENT PGAM 2) (MUSCLE-SPECIFIC PHOSPHOGLYCERATE MUTASE). [SWISSPROT;Acc:P15259]
0.107534	0.0370125	MSI2	0.344193464	164	MUSASHI 2 ISOFORM A. [RefSeq;Acc:NM_138962]
0.107847	0.0256535	SLC25A31	0.237869389	1695
0.107989	0.0252117	MRPL22	0.233465446	1845	MITOCHONDRIAL RIBOSOMAL PROTEIN L22. [RefSeq;Acc:NM_014180]
0.108089	0.0252313	FCF1	0.233430784	1857
0.108151	0.0263893	FA2H	0.244004216	1414	FATTY ACID HYDROXYLASE DOMAIN CONTAINING 1. [RefSeq;Acc:NM_024306]
0.108468	0.0266534	P4HA2	0.245725928	1305	"PROLYL 4-HYDROXYLASE ALPHA-2 SUBUNIT PRECURSOR (EC 1.14.11.2) (4-PH ALPHA-2) (PROCOLLAGEN-PROLINE,2-OXOGLUTARATE-4-DIOXYGENASE ALPHA-2 SUBUNIT). [SWISSPROT;Acc:O15460]"
0.109656	0.0258082	HSD17B1	0.235356022	1781	ESTRADIOL 17 BETA-DEHYDROGENASE 1 (EC 1.1.1.62) (17-BETA-HSD 1) (PLACENTAL 17-BETA-HYDROXYSTEROID DEHYDROGENASE) (20 ALPHA- HYDROXYSTEROID DEHYDROGENASE) (20-ALPHA-HSD) (E2DH). [SWISSPROT;Acc:P14061]
0.109803	0.0268629	GSK3A	0.244646321	1381	GLYCOGEN SYNTHASE KINASE-3 ALPHA (EC 2.7.1.37) (GSK-3 ALPHA). [SWISSPROT;Acc:P49840]
0.110346	0.0244744	SERPINB1	0.221796893	2319	LEUKOCYTE ELASTASE INHIBITOR (LEI) (MONOCYTE/NEUTROPHIL ELASTASE INHIBITOR) (M/NEI) (EI). [SWISSPROT;Acc:P30740]
0.1105	0.0289523	TEX28P2	0.262011765	803	TESTIS-SPECIFIC PROTEIN TEX28. [SWISSPROT;Acc:O15482]
0.110551	0.0281805	no value	0.254909499	1003	HUNTINGTIN INTERACTING PROTEIN E; HUNTINGTIN INTERACTOR PROTEIN E. [RefSeq;Acc:NM_007076]
0.110947	0.0334849	no value	0.301809873	287	"FATTY ACID-BINDING PROTEIN, EPIDERMAL (E-FABP) (PSORIASIS-ASSOCIATED FATTY ACID-BINDING PROTEIN HOMOLOG) (PA-FABP). [SWISSPROT;Acc:Q01469]"
0.11112	0.0280767	PDC	0.252670086	1058	PHOSDUCIN (PHD) (33 KDA PHOTOTRANSDUCING PROTEIN) (MEKA PROTEIN). [SWISSPROT;Acc:P20941]
0.111754	0.0244129	VPS8	0.218452136	2410
0.111754	0.0376993	FLNB	0.33734184	179	"FILAMIN B, BETA (ACTIN BINDING PROTEIN 278); BETA FILAMIN; FILAMIN 1 (ACTIN-BINDING PROTEIN-280)-LIKE; FILAMIN B, BETA (ACTIN-BINDING PROTEIN-278); FILAMIN B, BETA. [RefSeq;Acc:NM_001457]"
0.111998	0.0254509	SPCS2	0.227244237	2158	MICROSOMAL SIGNAL PEPTIDASE 25 KDA SUBUNIT (EC 3.4.-.-) (SPASE 25 KDA SUBUNIT) (SPC25). [SWISSPROT;Acc:Q15005]
0.112006	0.0271819	ZRF1	0.242682535	1503	ZUOTIN RELATED FACTOR-1 (M-PHASE PHOSPHOPROTEIN 11). [SWISSPROT;Acc:Q99543]
0.1121	0.0296502	no value	0.26449777	745	BA508N22.1 (HSPC025) (FRAGMENT). [SPTREMBL;Acc:Q9HCW5]
0.112137	0.0240826	no value	0.214760516	2533	KERATIN ASSOCIATED PROTEIN 2-4; KERATIN ASSOCIATED PROTEIN 2.4. [RefSeq;Acc:NM_033184]
0.112542	0.0256791	DPY19L1	0.228173482	2118
0.112547	0.0267969	NEK3	0.238095196	1688	SERINE/THREONINE-PROTEIN KINASE NEK3 (EC 2.7.1.37) (NIMA-RELATED PROTEIN KINASE 3) (HSPK 36). [SWISSPROT;Acc:P51956]
0.113378	0.0382473	PRMT8	0.337343224	175	PROTEIN ARGININE N-METHYLTRANSFERASE 4 (EC 2.1.1.-). [SWISSPROT;Acc:Q9NR22]
0.113537	0.0296703	MYL6	0.261327144	818	"MYOSIN LIGHT CHAIN 1, SLOW-TWITCH MUSCLE A ISOFORM (MLC1SA) (ALKALI). [SWISSPROT;Acc:P14649]"
0.113537	0.0296703	NDUFS6	0.261327144	817	"NADH-UBIQUINONE OXIDOREDUCTASE 13 KDA-A SUBUNIT, MITOCHONDRIAL PRECURSOR (EC 1.6.5.3) (EC 1.6.99.3) (COMPLEX I-13KD-A) (CI-13KD-A). [SWISSPROT;Acc:O75380]"
0.113606	0.0233268	VAMP1	0.205330704	2734	VESICLE-ASSOCIATED MEMBRANE PROTEIN 1 (VAMP-1) (SYNAPTOBREVIN 1). [SWISSPROT;Acc:P23763]
0.114139	0.0249219	SERINC2	0.218346928	2414	TUMOR DIFFERENTIALLY EXPRESSED PROTEIN 2. [RefSeq;Acc:NM_178865]
0.114163	0.0298281	no value	0.261276421	827	PUTATIVE ANKYRIN-REPEAT CONTAINING PROTEIN. [RefSeq;Acc:NM_025185]
0.11461	0.0230825	LYPLA1	0.201400401	2772	LYSOPHOSPHOLIPASE I; LYSOPHOSPHOLIPASE 1; LYSOPHOSPHOLIPID-SPECIFIC LYSOPHOSPHOLIPASE; ACYL-PROTEIN THIOESTERASE-1. [RefSeq;Acc:NM_006330]
0.11461	0.0230825	PBLD	0.201400401	2771	MAWD BINDING PROTEIN (UNKNOWN PROTEIN 32 FROM 2D-PAGE OF LIVER TISSUE). [SWISSPROT;Acc:P30039]
0.114679	0.0299629	STARD3NL	0.261276258	828	MLN64 N-TERMINAL DOMAIN HOMOLOG (STARD3 N-TERMINAL LIKE PROTEIN). [SWISSPROT;Acc:O95772]
0.114733	0.0267948	C18orf22	0.233540481	1840
0.114745	0.0283804	AURKC	0.247334524	1254	SERINE/THREONINE PROTEIN KINASE 13 (EC 2.7.1.37) (AURORA/IPL1/EG2 PROTEIN 2) (AURORA/IPL1-RELATED KINASE 3) (AURORA-C). [SWISSPROT;Acc:Q9UQB9]
0.114826	0.0300014	FAT2	0.261277063	822	PROTOCADHERIN FAT 2 PRECURSOR (HFAT2) (MULTIPLE EPIDERMAL GROWTH FACTOR-LIKE DOMAINS 1). [SWISSPROT;Acc:Q9NYQ8]
0.115005	0.0274831	ADCK4	0.238973088	1653	AARF DOMAIN CONTAINING KINASE 4. [RefSeq;Acc:NM_024876]
0.115107	0.0241725	DLC1	0.210000261	2621	RHO-GTPASE-ACTIVATING PROTEIN 7 (RHO-TYPE GTPASE-ACTIVATING PROTEIN 7) (DELETED IN LIVER CANCER 1 PROTEIN) (DLC-1) (HP PROTEIN) (STAR-RELATED LIPID TRANSFER PROTEIN 12) (STARD12) (START DOMAIN-CONTAINING PROTEIN 12). [SWISSPROT;Acc:Q96QB1]
0.115136	0.0241785	SPHK1	0.209999479	2623	SPHINGOSINE KINASE 1 (EC 2.7.1.-) (SK 1) (SPK 1). [SWISSPROT;Acc:Q9NYA1]

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Hugo is the bloody hugo identifier as demanded by the BMC Bioinformatics idiots

- http://analysis.yellowcouch.org/