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 Gene Rank Hugo description measured final
Results: HTML CSV LaTeX Showing element 101 to 150 of 3206 in total
expected
Rank
Hugo
description
measured
final
0.104721 3199 CHMP2B 0.00386024 0.036862138
0.104827 2735 VAMP3 VESICLE-ASSOCIATED MEMBRANE PROTEIN 3 (VAMP-3) (SYNAPTOBREVIN 3) (CELLUBREVIN) (CEB). [SWISSPROT;Acc:Q15836] 0.0215242 0.205330688
0.104865 2589 SLC25A13 "CALCIUM-BINDING MITOCHONDRIAL CARRIER PROTEIN ARALAR2 (SOLUTE CARRIER FAMILY 25, MEMBER 13) (CITRIN). [SWISSPROT;Acc:Q9UJS0]" 0.0223249 0.212891813
0.104981 1931 FAM98B 0.0243256 0.23171431
0.105024 1443 COQ2 0.0255702 0.243470064
0.105517 1782 no value 17 BETA-HYDROXYSTEROID DEHYDROGENASE. [SPTREMBL;Acc:Q13034] 0.024834 0.23535544
0.105559 1511 NGDN 0.0256005 0.242523139
0.105652 1528 NET1 NEUROEPITHELIAL CELL TRANSFORMING GENE 1; GUANINE NUCLEOTIDE REGULATORY PROTEIN (ONCOGENE); RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR (GEF) 8. [RefSeq;Acc:NM_005863] 0.0256013 0.24231723
0.106604 1410 HS6ST2 HEPARAN SULFATE 6-O-SULFOTRANSFERASE 2. [RefSeq;Acc:NM_147174] 0.0260119 0.244004915
0.106609 913 SLC37A1 GLYCEROL-3-PHOSPHATE TRANSPORTER (G-3-P TRANSPORTER) (G-3-P PERMEASE). [SWISSPROT;Acc:P57057] 0.0275088 0.2580345
0.106724 2212 NUCB1 NUCLEOBINDIN 1 PRECURSOR (CALNUC). [SWISSPROT;Acc:Q02818] 0.0240186 0.225053409
0.106766 659 no value SECRETED MODULAR CALCIUM-BINDING PROTEIN 1. [RefSeq;Acc:NM_022137] 0.0285187 0.267114063
0.106779 2116 DPY19L2P2 0.0243642 0.228174079
0.10746 1096 PGAM2 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] 0.0270059 0.251311186
0.107534 164 MSI2 MUSASHI 2 ISOFORM A. [RefSeq;Acc:NM_138962] 0.0370125 0.344193464
0.107847 1695 SLC25A31 0.0256535 0.237869389
0.107989 1845 MRPL22 MITOCHONDRIAL RIBOSOMAL PROTEIN L22. [RefSeq;Acc:NM_014180] 0.0252117 0.233465446
0.108089 1857 FCF1 0.0252313 0.233430784
0.108151 1414 FA2H FATTY ACID HYDROXYLASE DOMAIN CONTAINING 1. [RefSeq;Acc:NM_024306] 0.0263893 0.244004216
0.108468 1305 P4HA2 "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]" 0.0266534 0.245725928
0.109656 1781 HSD17B1 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] 0.0258082 0.235356022
0.109803 1381 GSK3A GLYCOGEN SYNTHASE KINASE-3 ALPHA (EC 2.7.1.37) (GSK-3 ALPHA). [SWISSPROT;Acc:P49840] 0.0268629 0.244646321
0.110346 2319 SERPINB1 LEUKOCYTE ELASTASE INHIBITOR (LEI) (MONOCYTE/NEUTROPHIL ELASTASE INHIBITOR) (M/NEI) (EI). [SWISSPROT;Acc:P30740] 0.0244744 0.221796893
0.1105 803 TEX28P2 TESTIS-SPECIFIC PROTEIN TEX28. [SWISSPROT;Acc:O15482] 0.0289523 0.262011765
0.110551 1003 no value HUNTINGTIN INTERACTING PROTEIN E; HUNTINGTIN INTERACTOR PROTEIN E. [RefSeq;Acc:NM_007076] 0.0281805 0.254909499
0.110947 287 "FATTY ACID-BINDING PROTEIN, EPIDERMAL (E-FABP) (PSORIASIS-ASSOCIATED FATTY ACID-BINDING PROTEIN HOMOLOG) (PA-FABP). [SWISSPROT;Acc:Q01469]" 0.0334849 0.301809873
0.11112 1058 PDC PHOSDUCIN (PHD) (33 KDA PHOTOTRANSDUCING PROTEIN) (MEKA PROTEIN). [SWISSPROT;Acc:P20941] 0.0280767 0.252670086
0.111754 179 FLNB "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]" 0.0376993 0.33734184
2410 VPS8 0.0244129 0.218452136
0.111998 2158 SPCS2 MICROSOMAL SIGNAL PEPTIDASE 25 KDA SUBUNIT (EC 3.4.-.-) (SPASE 25 KDA SUBUNIT) (SPC25). [SWISSPROT;Acc:Q15005] 0.0254509 0.227244237
0.112006 1503 ZRF1 ZUOTIN RELATED FACTOR-1 (M-PHASE PHOSPHOPROTEIN 11). [SWISSPROT;Acc:Q99543] 0.0271819 0.242682535
0.1121 745 no value BA508N22.1 (HSPC025) (FRAGMENT). [SPTREMBL;Acc:Q9HCW5] 0.0296502 0.26449777
0.112137 2533 KERATIN ASSOCIATED PROTEIN 2-4; KERATIN ASSOCIATED PROTEIN 2.4. [RefSeq;Acc:NM_033184] 0.0240826 0.214760516
0.112542 2118 DPY19L1 0.0256791 0.228173482
0.112547 1688 NEK3 SERINE/THREONINE-PROTEIN KINASE NEK3 (EC 2.7.1.37) (NIMA-RELATED PROTEIN KINASE 3) (HSPK 36). [SWISSPROT;Acc:P51956] 0.0267969 0.238095196
0.113378 175 PRMT8 PROTEIN ARGININE N-METHYLTRANSFERASE 4 (EC 2.1.1.-). [SWISSPROT;Acc:Q9NR22] 0.0382473 0.337343224
0.113537 817 NDUFS6 "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]" 0.0296703 0.261327144
818 MYL6 "MYOSIN LIGHT CHAIN 1, SLOW-TWITCH MUSCLE A ISOFORM (MLC1SA) (ALKALI). [SWISSPROT;Acc:P14649]"
0.113606 2734 VAMP1 VESICLE-ASSOCIATED MEMBRANE PROTEIN 1 (VAMP-1) (SYNAPTOBREVIN 1). [SWISSPROT;Acc:P23763] 0.0233268 0.205330704
0.114139 2414 SERINC2 TUMOR DIFFERENTIALLY EXPRESSED PROTEIN 2. [RefSeq;Acc:NM_178865] 0.0249219 0.218346928
0.114163 827 no value PUTATIVE ANKYRIN-REPEAT CONTAINING PROTEIN. [RefSeq;Acc:NM_025185] 0.0298281 0.261276421
0.11461 2771 PBLD MAWD BINDING PROTEIN (UNKNOWN PROTEIN 32 FROM 2D-PAGE OF LIVER TISSUE). [SWISSPROT;Acc:P30039] 0.0230825 0.201400401
2772 LYPLA1 LYSOPHOSPHOLIPASE I; LYSOPHOSPHOLIPASE 1; LYSOPHOSPHOLIPID-SPECIFIC LYSOPHOSPHOLIPASE; ACYL-PROTEIN THIOESTERASE-1. [RefSeq;Acc:NM_006330]
0.114679 828 STARD3NL MLN64 N-TERMINAL DOMAIN HOMOLOG (STARD3 N-TERMINAL LIKE PROTEIN). [SWISSPROT;Acc:O95772] 0.0299629 0.261276258
0.114733 1840 C18orf22 0.0267948 0.233540481
0.114745 1254 AURKC 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] 0.0283804 0.247334524
0.114826 822 FAT2 PROTOCADHERIN FAT 2 PRECURSOR (HFAT2) (MULTIPLE EPIDERMAL GROWTH FACTOR-LIKE DOMAINS 1). [SWISSPROT;Acc:Q9NYQ8] 0.0300014 0.261277063
0.115005 1653 ADCK4 AARF DOMAIN CONTAINING KINASE 4. [RefSeq;Acc:NM_024876] 0.0274831 0.238973088
0.115107 2621 DLC1 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] 0.0241725 0.210000261
0.115136 2623 SPHK1 SPHINGOSINE KINASE 1 (EC 2.7.1.-) (SK 1) (SPK 1). [SWISSPROT;Acc:Q9NYA1] 0.0241785 0.209999479

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/