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

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/