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 Rank Gene description measured final Hugo
Results: HTML CSV LaTeX Showing element 902 to 951 of 3206 in total
expected
Rank
description
measured
final
Hugo
0.269788 1885 DIMETHYLANILINE MONOOXYGENASE [N-OXIDE FORMING] 5 (EC 1.14.13.8) (HEPATIC FLAVIN-CONTAINING MONOOXYGENASE 5) (FMO 5) (DIMETHYLANILINE OXIDASE 5). [SWISSPROT;Acc:P49326] 0.0627928 0.232748677 FMO5
0.269823 1876 SARCOGLYCAN ZETA; ZETA-SARCOGLYCAN. [RefSeq;Acc:NM_139167] 0.0628075 0.232772966 SGCZ
0.270114 1464 DEFORMED EPIDERMAL AUTOREGULATORY FACTOR 1 HOMOLOG (NUCLEAR DEAF-1 RELATED TRANSCRIPTIONAL REGULATOR) (NUDR) (SUPPRESSIN) (ZINC FINGER MYND DOMAIN CONTAINING PROTEIN 5). [SWISSPROT;Acc:O75398] 0.0656459 0.24303035 DEAF1
0.270441 1395 MYOSIN VIIA. [SWISSPROT;Acc:Q13402] 0.066057 0.244256603 MYO7A
0.270506 2574 0.0577101 0.213341294 no value
0.270652 2476 0.0586202 0.21658883 LSM14A
0.270962 1878 DELTA-SARCOGLYCAN (SG-DELTA) (35 KDA DYSTROPHIN-ASSOCIATED GLYCOPROTEIN) (35DAG). [SWISSPROT;Acc:Q92629] 0.0630725 0.232772492 SGCD
0.271164 2189 DNA-BINDING PROTEIN A (COLD SHOCK DOMAIN PROTEIN A) (SINGLE-STRAND DNA BINDING PROTEIN NF-GMB). [SWISSPROT;Acc:P16989] 0.0613805 0.226359325 CSDA
0.271247 1584 HURPIN (HACAT UV-REPRESSIBLE SERPIN) (PROTEASE INHIBITOR 13) (HEADPIN) (SERPIN B13). [SWISSPROT;Acc:Q9UIV8] 0.0653411 0.240891512 no value
0.271591 2998 SOURCE OF IMMUNODOMINANT MHC-ASSOCIATED PEPTIDES; HOMOLOG OF YEAST STT3 GENE. [RefSeq;Acc:NM_178862] 0.0366899 0.135092474 STT3B
0.271808 2746 GLUTAMATE--CYSTEINE LIGASE REGULATORY SUBUNIT (EC 6.3.2.2) (GAMMA- GLUTAMYLCYSTEINE SYNTHETASE) (GAMMA-ECS) (GCS LIGHT CHAIN) (GLUTAMATE--CYSTEINE LIGASE MODIFIER SUBUNIT). [SWISSPROT;Acc:P48507] 0.0555879 0.204511641 GCLM
0.272436 1056 REPLICATION PROTEIN A 70 KDA DNA-BINDING SUBUNIT (RP-A) (RF-A) (REPLICATION FACTOR-A PROTEIN 1) (SINGLE-STRANDED DNA-BINDING PROTEIN). [SWISSPROT;Acc:P27694] 0.0688366 0.252670719 RPA1
0.272579 2122 DEFENDER AGAINST CELL DEATH 1 (DAD-1). [SWISSPROT;Acc:P46966] 0.0621814 0.228122489 DAD1
0.272797 2509 D(4) DOPAMINE RECEPTOR (D(2C) DOPAMINE RECEPTOR). [SWISSPROT;Acc:P21917] 0.0585879 0.214767391 DRD4
0.27327 1755 APOPTOSIS INHIBITOR 5; FIBROBLAST GROWTH FACTOR 2-INTERACTING FACTOR 2; API5-LIKE 1. [RefSeq;Acc:NM_006595] 0.0646874 0.236716068 API5
0.273711 1223 DEAD-BOX PROTEIN 4 (VASA HOMOLOG). [SWISSPROT;Acc:Q9NQI0] 0.0678848 0.248016338 DDX4
0.273869 3198 PUTATIVE BREAST ADENOCARCINOMA MARKER (32KD). [RefSeq;Acc:NM_014453] 0.0100954 0.036862149 CHMP2A
0.274218 2366 PEPSIN A PRECURSOR (EC 3.4.23.1). [SWISSPROT;Acc:P00790] 0.0604093 0.220296625 no value
0.274826 1910 "PEROXIREDOXIN 5, MITOCHONDRIAL PRECURSOR (PRX-V) (PEROXISOMAL ANTIOXIDANT ENZYME) (PLP) (THIOREDOXIN PEROXIDASE PMP20) (ANTIOXIDANT ENZYME B166) (AOEB166) (TPX TYPE VI) (LIVER TISSUE 2D-PAGE SPOT 71B) (ALU CO-REPRESSOR 1) (SBBI10). [SWISSPROT;Acc:P" 0.0637963 0.232133423 PRDX5
0.274876 158 NEURALIZED-LIKE. [RefSeq;Acc:NM_004210] 0.096416 0.350761798 NEURL
0.274937 3050 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(O) GAMMA-11 SUBUNIT. [SWISSPROT;Acc:P50152] 0.0293247 0.106659707 GNG11
0.276021 2136 0.0629265 0.227977219 BSCL2
0.276631 2152 PP1201 PROTEIN. [RefSeq;Acc:NM_022152] 0.0628846 0.22732304 TMBIM1
0.277203 1772 HEAT SHOCK 70 KDA PROTEIN 1 (HSP70.1) (HSP70-1/HSP70-2). [SWISSPROT;Acc:P08107] 0.0654179 0.235992756 no value
0.27731 2340 TYPE 1 PROTEIN PHOSPHATASE INHIBITOR. [RefSeq;Acc:NM_025210] 0.0612127 0.220737442 PPP1R2P9
0.277567 1202 0.0689331 0.248347606 TMTC4
0.277887 851 CONSERVED OLIGOMERIC GOLGI COMPLEX COMPONENT 2 (LOW DENSITY LIPOPROTEIN RECEPTOR DEFECT C-COMPLEMENTING PROTEIN). [SWISSPROT;Acc:Q14746] 0.0723993 0.260535038 COG2
0.278146 2880 0.0513128 0.184481531 CXorf56
2881 ADAPTER-RELATED PROTEIN COMPLEX 3 BETA 2 SUBUNIT (BETA-ADAPTIN 3B) (AP-3 COMPLEX BETA-3B SUBUNIT) (BETA-3B-ADAPTIN) (NEURON-SPECIFIC VESICLE COAT PROTEIN BETA-NAP). [SWISSPROT;Acc:Q13367] no value
0.278552 2516 STAR-RELATED LIPID TRANSFER PROTEIN 5 (STARD5) (START DOMAIN- CONTAINING PROTEIN 5). [SWISSPROT;Acc:Q9NSY2] 0.0598238 0.214767081 STARD5
2517 C11orf46
2518 RAS-GTPASE-ACTIVATING PROTEIN BINDING PROTEIN 2 (GAP SH3-DOMAIN BINDING PROTEIN 2) (G3BP-2). [SWISSPROT;Acc:Q9UN86] G3BP2
0.278747 2791 TRAP/MEDIATOR COMPLEX COMPONENT TRAP25. [RefSeq;Acc:NM_080651] 0.0557223 0.199902779 MED30
0.278835 314 PROTEIN CGI-147. [SWISSPROT;Acc:Q9Y3E5] 0.0820629 0.29430631 PTRH2
0.278856 1517 GLIA MATURATION FACTOR GAMMA (GMF-GAMMA). [SWISSPROT;Acc:O60234] 0.0675774 0.242337981 GMFG
0.278919 775 TRIPLE FUNCTIONAL DOMAIN PROTEIN (PTPRF INTERACTING PROTEIN). [SWISSPROT;Acc:O75962] 0.0734189 0.2632266 TRIO
0.279962 1770 HEAT SHOCK-RELATED 70 KDA PROTEIN 2 (HEAT SHOCK 70 KDA PROTEIN 2). [SWISSPROT;Acc:P54652] 0.0660691 0.235993099 HSPA2
0.279967 2515 ESPIN. [RefSeq;Acc:NM_031475] 0.0601277 0.214767098 ESPNP
0.280228 1245 "SOLUTE CARRIER FAMILY 2, FACILITATED GLUCOSE TRANSPORTER, MEMBER 8 (GLUCOSE TRANSPORTER TYPE 8) (GLUCOSE TRANSPORTER TYPE X1). [SWISSPROT;Acc:Q9NY64]" 0.069385 0.247601953 SLC2A8
0.280704 2127 "GLYCINE DEHYDROGENASE [DECARBOXYLATING], MITOCHONDRIAL PRECURSOR (EC 1.4.4.2) (GLYCINE DECARBOXYLASE) (GLYCINE CLEAVAGE SYSTEM P- PROTEIN). [SWISSPROT;Acc:P23378]" 0.0640341 0.228119656 no value
0.280936 46 HEPATOCYTE NUCLEAR FACTOR 4-GAMMA (HNF-4-GAMMA). [SWISSPROT;Acc:Q14541] 0.117156 0.417020247 HNF4G
0.280961 2042 GOODPASTURE ANTIGEN-BINDING PROTEIN (EC 2.7.1.37) (GPBP) (COLLAGEN TYPE IV ALPHA 3 BINDING PROTEIN) (STAR-RELATED LIPID TRANSFER PROTEIN 11) (STARD11) (START DOMAIN-CONTAINING PROTEIN 11). [SWISSPROT;Acc:Q9Y5P4] 0.0646597 0.230137635 COL4A3BP
0.282461 968 DNAJ HOMOLOG SUBFAMILY B MEMBER 5 (HEAT SHOCK PROTEIN HSP40-3) (HEAT SHOCK PROTEIN COGNATE 40) (HSC40) (HSP40-2). [SWISSPROT;Acc:O75953] 0.0721855 0.255559175 DNAJB5
969 DNAJ HOMOLOG SUBFAMILY B MEMBER 4 (HEAT SHOCK 40 KDA PROTEIN 1 HOMOLOG) (HEAT SHOCK PROTEIN 40 HOMOLOG) (HSP40 HOMOLOG). [SWISSPROT;Acc:Q9UDY4] DNAJB4
0.282946 2768 ZINC FINGER PROTEIN 277. [SWISSPROT;Acc:Q9NRM2] 0.0570468 0.20161727 no value
0.28346 718 INTERFERON-RELATED DEVELOPMENTAL REGULATOR 2 (SKMC15 PROTEIN). [SWISSPROT;Acc:Q12894] 0.0750554 0.264783038 HYAL3
0.285217 2108 0.0651212 0.228321594 PUS7
0.285269 2981 0.0398119 0.139559153 MTERFD1
0.2855 1742 CONSERVED OLIGOMERIC GOLGI COMPLEX COMPONENT 6. [SWISSPROT;Acc:Q9Y2V7] 0.0676104 0.236814011 COG6
0.285541 2169 GLYCOGENIN-1 (EC 2.4.1.186). [SWISSPROT;Acc:P46976] 0.0648248 0.22702449 GYG1

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/