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 measured description final Hugo expected
Results: HTML CSV LaTeX Showing element 951 to 1000 of 3206 in total
Rank
measured
description
final
Hugo
expected
951 0.0645342 "10 KDA HEAT SHOCK PROTEIN, MITOCHONDRIAL (HSP10) (10 KDA CHAPERONIN) (CPN10). [SWISSPROT;Acc:Q04984]" 0.25640555 HSPE1 0.251688
952 0.135079 SIMILAR TO PUTATIVE TRANSMEMBRANE PROTEIN; HOMOLOG OF YEAST GOLGI MEMBRANE PROTEIN YIF1P (YIP1P-INTERACTING FACTOR). [RefSeq;Acc:NM_033557] 0.256405438 YIF1B 0.526818
953 0.0261125 ALPHA/BETA HYDROLASE DOMAIN CONTAINING PROTEIN 1 ISOFORM 2; LUNG ALPHA/BETA HYDROLASE PROTEIN 1. [RefSeq;Acc:NM_152870] 0.256404591 ABHD1 0.101841
954 1.24311 IMPORTIN ALPHA-1 SUBUNIT (KARYOPHERIN ALPHA-1 SUBUNIT) (SRP1-BETA) (RAG COHORT PROTEIN 2) (NUCLEOPROTEIN INTERACTOR 1) (NPI-1). [SWISSPROT;Acc:P52294] 0.256363141 KPNA1 4.84902
955 0.209882 VACUOLAR PROTEIN SORTING 16 (HVPS16). [SWISSPROT;Acc:Q9H269] 0.256335974 PTPRA 0.818777
956 0.308685 60S RIBOSOMAL PROTEIN L24 (L30). [SWISSPROT;Acc:P38663] 0.256333923 RPL24 1.20423
957 0.288835 CTP SYNTHASE (EC 6.3.4.2) (UTP--AMMONIA LIGASE) (CTP SYNTHETASE). [SWISSPROT;Acc:P17812] 0.256304795 CTPS 1.12692
958 0.0783783 0.256286479 TIMM50 0.305823
959 0.226073 CYTIDINE TRIPHOSPHATE SYNTHASE II; CTP SYNTHETASE TYPE 2; UTP-AMMONIA LIGASE; CTP SYNTHETASE ISOFORM; CYTIDINE 5'-TRIPHOSPHATE SYNTHETASE 2. [RefSeq;Acc:NM_019857] 0.256264552 CTPS2 0.882186
960 0.0614814 "ACYL-COA DEHYDROGENASE, SHORT/BRANCHED CHAIN SPECIFIC, MITOCHONDRIAL PRECURSOR (EC 1.3.99.-) (SBCAD) (2-METHYL BRANCHED CHAIN ACYL-COA DEHYDROGENASE) (2-MEBCAD) (2-METHYLBUTYRYL-COENZYME A DEHYDROGENASE) (2-METHYLBUTYRYL-COA DEHYDROGENASE). [SWISSP" 0.256126611 no value 0.240043
961 0.909945 PDZ/COILED-COIL DOMAIN BINDING PARTNER FOR THE RHO-FAMILY GTPASE TC10; FUSED IN GLIOBLASTOMA; GOLGI ASSOCIATED PDZ AND COILED-COIL MOTIF CONTAINING PROTEIN; CFTR-ASSOCIATED LIGAND. [RefSeq;Acc:NM_020399] 0.256041971 GOPC 3.55389
962 0.0391646 PRIP-INTERACTING PROTEIN PIPMT; PRIP-INTERACTING PROTEIN WITH METHYLTRANSFERASE DOMAIN. [RefSeq;Acc:NM_024831] 0.25604137 TGS1 0.152962
963 C6orf32
964 0.031735 STRUCTURE-SPECIFIC RECOGNITION PROTEIN 1 (SSRP1) (RECOMBINATION SIGNAL SEQUENCE RECOGNITION PROTEIN) (T160) (CHROMATIN-SPECIFIC TRANSCRIPTION ELONGATION FACTOR 80 KDA SUBUNIT) (FACT 80 KDA SUBUNIT). [SWISSPROT;Acc:Q08945] 0.255927419 SSRP1 0.124
965 0.12694 CHROMATIN-SPECIFIC TRANSCRIPTION ELONGATION FACTOR LARGE SUBUNIT. [RefSeq;Acc:NM_007192] 0.255926903 SUPT16H 0.496001
966 0.553061 PROTEIN TRANSLATION FACTOR SUI1 HOMOLOG GC20. [SWISSPROT;Acc:O60739] 0.255827648 EIF1B 2.16185
967 0.100509 EUKARYOTIC PEPTIDE CHAIN RELEASE FACTOR SUBUNIT 1 (ERF1) (EUKARYOTIC RELEASE FACTOR 1) (TB3-1) (C11 PROTEIN). [SWISSPROT;Acc:P46055] 0.255559511 ETF1 0.39329
968 0.0721855 DNAJ HOMOLOG SUBFAMILY B MEMBER 5 (HEAT SHOCK PROTEIN HSP40-3) (HEAT SHOCK PROTEIN COGNATE 40) (HSC40) (HSP40-2). [SWISSPROT;Acc:O75953] 0.255559175 DNAJB5 0.282461
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
970 0.0366052 CAB2. [RefSeq;Acc:NM_033419] 0.255558658 PERLD1 0.143236
971 0.281375 SUPPRESSOR OF ACTIN MUTATIONS 2-LIKE ISOFORM B; DJ1033B10.5. [RefSeq;Acc:NM_022553] 0.255558482 VPS52 1.10102
972 0.0597214 DNAJ HOMOLOG SUBFAMILY B MEMBER 1 (HEAT SHOCK 40 KDA PROTEIN 1) (HEAT SHOCK PROTEIN 40) (HSP40) (DNAJ PROTEIN HOMOLOG 1) (HDJ-1). [SWISSPROT;Acc:P25685] 0.255558218 DNAJB1 0.23369
973 0.117727 G1 TO S PHASE TRANSITION PROTEIN 1 HOMOLOG (GTP-BINDING PROTEIN GST1-HS). [SWISSPROT;Acc:P15170] 0.255432943 GSPT1 0.460892
974 0.354858 TRANSDUCIN-LIKE ENHANCER PROTEIN 4. [SWISSPROT;Acc:Q04727] 0.255411125 TLE4 1.38936
975 0.095104 SON PROTEIN (SON3) (NEGATIVE REGULATORY ELEMENT-BINDING PROTEIN) (NRE- BINDING PROTEIN) (DBP-5) (BAX ANTAGONIST SELECTED IN SACCHAROMYCES 1) (BASS1) (PROTEIN C21ORF50). [SWISSPROT;Acc:P18583] 0.255408058 SON 0.372361
976 0.114475 60S ACIDIC RIBOSOMAL PROTEIN P2. [SWISSPROT;Acc:P05387] 0.255393436 RPLP2 0.44823
977 0.149858 TSC22-RELATED INDUCIBLE LEUCINE ZIPPER PROTEIN 2 (TSC-22-LIKE PROTEIN THG-1). [SWISSPROT;Acc:Q9Y3Q8] 0.255357362 TSC22D4 0.586856
978 0.0374644 SPHINGOLIPID DELTA 4 DESATURASE; MEMBRANE FATTY ACID (LIPID) DESATURASE; DIHYDROCERAMIDE DESATURASE. [RefSeq;Acc:NM_003676] 0.25535668 DEGS1 0.146714
979 0.136601 "FRUCTOSE-1,6-BISPHOSPHATASE (EC 3.1.3.11) (D-FRUCTOSE-1,6-BISPHOSPHATE 1-PHOSPHOHYDROLASE) (FBPASE). [SWISSPROT;Acc:P09467]" 0.255308929 FBP1 0.535042
980 0.32192 0.255279331 no value 1.26105
981 0.0395897 60 KDA TAT INTERACTIVE PROTEIN (TIP60) (HIV-1 TAT INTERACTIVE PROTEIN) (CPLA(2) INTERACTING PROTEIN). [SWISSPROT;Acc:Q92993] 0.255279075 HTATIP 0.155084
982 0.314547 SORTING NEXIN 6 (TRAF4-ASSOCIATED FACTOR 2). [SWISSPROT;Acc:Q9UNH7] 0.255249897 SNX6 1.23231
983 0.12174 "FRUCTOSE-1,6-BISPHOSPHATASE ISOZYME 2 (EC 3.1.3.11) (D-FRUCTOSE-1,6- BISPHOSPHATE 1-PHOSPHOHYDROLASE) (FBPASE). [SWISSPROT;Acc:O00757]" 0.255198725 FBP2 0.47704
984 0.333664 TRANSDUCIN-LIKE ENHANCER PROTEIN 3 (ESG3). [SWISSPROT;Acc:Q04726] 0.255180642 TLE3 1.30756
985 0.11603 CYTOKINE-LIKE NUCLEAR FACTOR N-PAC. [RefSeq;Acc:NM_032569] 0.255168577 no value 0.454719
986 0.087747 0.255168242 HECW2 0.343879
987 0.0349473 ACTIVATOR OF BASAL TRANSCRIPTION 1; TATA-BINDING PROTEIN-BINDING PROTEIN; BASAL TRANSCRIPTIONAL ACTIVATOR. [RefSeq;Acc:NM_013375] 0.255168008 ABT1 0.136958
988 0.0745937 HECT TYPE E3 UBIQUITIN LIGASE. [RefSeq;Acc:NM_015052] 0.255167754 HECW1 0.292332
989 0.0439174 CPG BINDING PROTEIN (PROTEIN CONTAINING PHD FINGER AND CXXC DOMAIN 1). [SWISSPROT;Acc:Q9P0U4] 0.255167565 CXXC1 0.172112
990 0.283289 HOMEOBOX PROTEIN ENGRAILED-2 (HU-EN-2). [SWISSPROT;Acc:P19622] 0.25516704 EN2 1.11021
991 0.0378287 "ALPHA-(1,6)-FUCOSYLTRANSFERASE (EC 2.4.1.68) (GLYCOPROTEIN 6-ALPHA-L- FUCOSYLTRANSFERASE) (GDP-FUCOSE--GLYCOPROTEIN FUCOSYLTRANSFERASE) (GDP-L-FUC:N-ACETYL-BETA-D-GLUCOSAMINIDE ALPHA1,6-FUCOSYLTRANSFERASE) (ALPHA1-6FUCT) (FUCOSYLTRANSFERASE 8). [SW" 0.255053028 FUT8 0.148317
992 0.0744186 INOSITOL POLYPHOSPHATE MULTIKINASE. [RefSeq;Acc:NM_152230] 0.255053003 IPMK 0.291777
993 0.282136 AFG3-LIKE PROTEIN 2 (EC 3.4.24.-) (PARAPLEGIN-LIKE PROTEIN). [SWISSPROT;Acc:Q9Y4W6] 0.255052025 AFG3L2 1.10619
994 0.753893 PROTEASOME SUBUNIT BETA TYPE 4 PRECURSOR (EC 3.4.25.1) (PROTEASOME BETA CHAIN) (MACROPAIN BETA CHAIN) (MULTICATALYTIC ENDOPEPTIDASE COMPLEX BETA CHAIN) (PROTEASOME CHAIN 3) (HSN3) (HSBPROS26). [SWISSPROT;Acc:P28070] 0.255042541 PSMB4 2.95595
995 0.357881 TRANSDUCIN-LIKE ENHANCER PROTEIN 1 (ESG1). [SWISSPROT;Acc:Q04724] 0.255026331 no value 1.40331
996 0.304091 TRANSDUCIN-LIKE ENHANCER PROTEIN 2 (ESG2). [SWISSPROT;Acc:Q04725] 0.255011489 TLE2 1.19246
997 0.226174 RIBONUCLEOTIDE REDUCTASE M2 B (TP53 INDUCIBLE); P53-INDUCIBLE RIBONUCLEOTIDE REDUCTASE SMALL SUBUNIT 2 HOMOLOG. [RefSeq;Acc:NM_015713] 0.255004848 RRM2B 0.88694
998 0.115392 0.254913613 NUAK2 0.452671
999 0.036112 "N-ACETYLLACTOSAMINIDE BETA-1,3-N-ACETYLGLUCOSAMINYLTRANSFERASE (EC 2.4.1.149) (POLY-N-ACETYLLACTOSAMINE EXTENSION ENZYME) (I-BETA- 1,3-N-ACETYLGLUCOSAMINYLTRANSFERASE) (IGNT) (UDP-GLCNAC:BETAGAL BETA- 1,3-N-ACETYLGLUCOSAMINYLTRANSFERASE 6). [SWISSP" 0.254911234 B3GNT1 0.141665
1000 0.143571 0.254911047 ISOC2 0.56322

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/