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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Rank Gene expected description measured Hugo final
Results: HTML CSV LaTeX Showing element 951 to 1000 of 3206 in total
Rank
expected
description
measured
Hugo
final
951 0.251688 "10 KDA HEAT SHOCK PROTEIN, MITOCHONDRIAL (HSP10) (10 KDA CHAPERONIN) (CPN10). [SWISSPROT;Acc:Q04984]" 0.0645342 HSPE1 0.25640555
952 0.526818 SIMILAR TO PUTATIVE TRANSMEMBRANE PROTEIN; HOMOLOG OF YEAST GOLGI MEMBRANE PROTEIN YIF1P (YIP1P-INTERACTING FACTOR). [RefSeq;Acc:NM_033557] 0.135079 YIF1B 0.256405438
953 0.101841 ALPHA/BETA HYDROLASE DOMAIN CONTAINING PROTEIN 1 ISOFORM 2; LUNG ALPHA/BETA HYDROLASE PROTEIN 1. [RefSeq;Acc:NM_152870] 0.0261125 ABHD1 0.256404591
954 4.84902 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 0.256363141
955 0.818777 VACUOLAR PROTEIN SORTING 16 (HVPS16). [SWISSPROT;Acc:Q9H269] 0.209882 PTPRA 0.256335974
956 1.20423 60S RIBOSOMAL PROTEIN L24 (L30). [SWISSPROT;Acc:P38663] 0.308685 RPL24 0.256333923
957 1.12692 CTP SYNTHASE (EC 6.3.4.2) (UTP--AMMONIA LIGASE) (CTP SYNTHETASE). [SWISSPROT;Acc:P17812] 0.288835 CTPS 0.256304795
958 0.305823 0.0783783 TIMM50 0.256286479
959 0.882186 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 0.256264552
960 0.240043 "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 0.256126611
961 3.55389 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 0.256041971
962 0.152962 PRIP-INTERACTING PROTEIN PIPMT; PRIP-INTERACTING PROTEIN WITH METHYLTRANSFERASE DOMAIN. [RefSeq;Acc:NM_024831] 0.0391646 TGS1 0.25604137
963 C6orf32
964 0.124 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 0.255927419
965 0.496001 CHROMATIN-SPECIFIC TRANSCRIPTION ELONGATION FACTOR LARGE SUBUNIT. [RefSeq;Acc:NM_007192] 0.12694 SUPT16H 0.255926903
966 2.16185 PROTEIN TRANSLATION FACTOR SUI1 HOMOLOG GC20. [SWISSPROT;Acc:O60739] 0.553061 EIF1B 0.255827648
967 0.39329 EUKARYOTIC PEPTIDE CHAIN RELEASE FACTOR SUBUNIT 1 (ERF1) (EUKARYOTIC RELEASE FACTOR 1) (TB3-1) (C11 PROTEIN). [SWISSPROT;Acc:P46055] 0.100509 ETF1 0.255559511
968 0.282461 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 0.255559175
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 0.143236 CAB2. [RefSeq;Acc:NM_033419] 0.0366052 PERLD1 0.255558658
971 1.10102 SUPPRESSOR OF ACTIN MUTATIONS 2-LIKE ISOFORM B; DJ1033B10.5. [RefSeq;Acc:NM_022553] 0.281375 VPS52 0.255558482
972 0.23369 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 0.255558218
973 0.460892 G1 TO S PHASE TRANSITION PROTEIN 1 HOMOLOG (GTP-BINDING PROTEIN GST1-HS). [SWISSPROT;Acc:P15170] 0.117727 GSPT1 0.255432943
974 1.38936 TRANSDUCIN-LIKE ENHANCER PROTEIN 4. [SWISSPROT;Acc:Q04727] 0.354858 TLE4 0.255411125
975 0.372361 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 0.255408058
976 0.44823 60S ACIDIC RIBOSOMAL PROTEIN P2. [SWISSPROT;Acc:P05387] 0.114475 RPLP2 0.255393436
977 0.586856 TSC22-RELATED INDUCIBLE LEUCINE ZIPPER PROTEIN 2 (TSC-22-LIKE PROTEIN THG-1). [SWISSPROT;Acc:Q9Y3Q8] 0.149858 TSC22D4 0.255357362
978 0.146714 SPHINGOLIPID DELTA 4 DESATURASE; MEMBRANE FATTY ACID (LIPID) DESATURASE; DIHYDROCERAMIDE DESATURASE. [RefSeq;Acc:NM_003676] 0.0374644 DEGS1 0.25535668
979 0.535042 "FRUCTOSE-1,6-BISPHOSPHATASE (EC 3.1.3.11) (D-FRUCTOSE-1,6-BISPHOSPHATE 1-PHOSPHOHYDROLASE) (FBPASE). [SWISSPROT;Acc:P09467]" 0.136601 FBP1 0.255308929
980 1.26105 0.32192 no value 0.255279331
981 0.155084 60 KDA TAT INTERACTIVE PROTEIN (TIP60) (HIV-1 TAT INTERACTIVE PROTEIN) (CPLA(2) INTERACTING PROTEIN). [SWISSPROT;Acc:Q92993] 0.0395897 HTATIP 0.255279075
982 1.23231 SORTING NEXIN 6 (TRAF4-ASSOCIATED FACTOR 2). [SWISSPROT;Acc:Q9UNH7] 0.314547 SNX6 0.255249897
983 0.47704 "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 0.255198725
984 1.30756 TRANSDUCIN-LIKE ENHANCER PROTEIN 3 (ESG3). [SWISSPROT;Acc:Q04726] 0.333664 TLE3 0.255180642
985 0.454719 CYTOKINE-LIKE NUCLEAR FACTOR N-PAC. [RefSeq;Acc:NM_032569] 0.11603 no value 0.255168577
986 0.343879 0.087747 HECW2 0.255168242
987 0.136958 ACTIVATOR OF BASAL TRANSCRIPTION 1; TATA-BINDING PROTEIN-BINDING PROTEIN; BASAL TRANSCRIPTIONAL ACTIVATOR. [RefSeq;Acc:NM_013375] 0.0349473 ABT1 0.255168008
988 0.292332 HECT TYPE E3 UBIQUITIN LIGASE. [RefSeq;Acc:NM_015052] 0.0745937 HECW1 0.255167754
989 0.172112 CPG BINDING PROTEIN (PROTEIN CONTAINING PHD FINGER AND CXXC DOMAIN 1). [SWISSPROT;Acc:Q9P0U4] 0.0439174 CXXC1 0.255167565
990 1.11021 HOMEOBOX PROTEIN ENGRAILED-2 (HU-EN-2). [SWISSPROT;Acc:P19622] 0.283289 EN2 0.25516704
991 0.148317 "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 0.255053028
992 0.291777 INOSITOL POLYPHOSPHATE MULTIKINASE. [RefSeq;Acc:NM_152230] 0.0744186 IPMK 0.255053003
993 1.10619 AFG3-LIKE PROTEIN 2 (EC 3.4.24.-) (PARAPLEGIN-LIKE PROTEIN). [SWISSPROT;Acc:Q9Y4W6] 0.282136 AFG3L2 0.255052025
994 2.95595 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 0.255042541
995 1.40331 TRANSDUCIN-LIKE ENHANCER PROTEIN 1 (ESG1). [SWISSPROT;Acc:Q04724] 0.357881 no value 0.255026331
996 1.19246 TRANSDUCIN-LIKE ENHANCER PROTEIN 2 (ESG2). [SWISSPROT;Acc:Q04725] 0.304091 TLE2 0.255011489
997 0.88694 RIBONUCLEOTIDE REDUCTASE M2 B (TP53 INDUCIBLE); P53-INDUCIBLE RIBONUCLEOTIDE REDUCTASE SMALL SUBUNIT 2 HOMOLOG. [RefSeq;Acc:NM_015713] 0.226174 RRM2B 0.255004848
998 0.452671 0.115392 NUAK2 0.254913613
999 0.141665 "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 0.254911234
1000 0.56322 0.143571 ISOC2 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/