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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Hugo measured Rank Gene description expected final
Results: HTML CSV LaTeX Showing element 1051 to 1100 of 3206 in total
Hugo
measured
Rank
description
expected
final
DNAJB4 0.0721855 969 DNAJ HOMOLOG SUBFAMILY B MEMBER 4 (HEAT SHOCK 40 KDA PROTEIN 1 HOMOLOG) (HEAT SHOCK PROTEIN 40 HOMOLOG) (HSP40 HOMOLOG). [SWISSPROT;Acc:Q9UDY4] 0.282461 0.255559175
DNAJB5 968 DNAJ HOMOLOG SUBFAMILY B MEMBER 5 (HEAT SHOCK PROTEIN HSP40-3) (HEAT SHOCK PROTEIN COGNATE 40) (HSC40) (HSP40-2). [SWISSPROT;Acc:O75953]
DNAJC12 0.155654 214 J DOMAIN CONTAINING PROTEIN 1. [SWISSPROT;Acc:Q9UKB3] 0.485577 0.320554721
DNALI1 0.124723 2195 "AXONEMAL DYNEIN LIGHT INTERMEDIATE POLYPEPTIDE 1 (INNER DYNEIN ARM LIGHT CHAIN, AXONEMAL) (HP28). [SWISSPROT;Acc:O14645]" 0.551845 0.226010927
DNASE2B 0.0586001 3085 DEOXYRIBONUCLEASE II BETA ISOFORM 1 PRECURSOR; DEOXYRIBONUCLEASE II BETA; ENDONUCLEASE DLAD. [RefSeq;Acc:NM_021233] 0.589168 0.099462462
DNM1L 0.121609 880 DYNAMIN 1-LIKE PROTEIN ISOFORM 3; DYNAMIN-LIKE PROTEIN. [RefSeq;Acc:NM_005690] 0.467587 0.260077804
DOHH 0.22609 1994 0.979382 0.230849658
DOK1 0.0754466 29 DOCKING PROTEIN 1 (P62(DOK)) (DOWNSTREAM OF TYROSINE KINASE 1) (PP62). [SWISSPROT;Acc:Q99704] 0.177056 0.426117161
DOK2 0.0954445 26 DOCKING PROTEIN 2 (P56(DOK-2)) (DOWNSTREAM OF TYROSINE KINASE 2). [SWISSPROT;Acc:O60496] 0.223986 0.42611815
DOLK 0.031449 1863 0.134819 0.233268308
DPAGT1 0.0686246 2627 UDP-N-ACETYLGLUCOSAMINE--DOLICHYL-PHOSPHATE N- ACETYLGLUCOSAMINEPHOSPHOTRANSFERASE (EC 2.7.8.15) (GPT) (G1PT) (N-ACETYLGLUCOSAMINE-1-PHOSPHATE TRANSFERASE) (GLCNAC-1-P TRANSFERASE). [SWISSPROT;Acc:Q9H3H5] 0.326785 0.209999235
DPH1 0.322756 2329 CANDIDATE TUMOR SUPPRESSOR IN OVARIAN CANCER 2. [RefSeq;Acc:NM_080822] 1.45734 0.221469252
DPH2 0.346955 2278 DIPHTHAMIDE BIOSYNTHESIS-LIKE PROTEIN 2. [RefSeq;Acc:NM_001384] 1.55897 0.222553994
DPM1 0.349731 2829 DOLICHOL-PHOSPHATE MANNOSYLTRANSFERASE (EC 2.4.1.83) (DOLICHOL- PHOSPHATE MANNOSE SYNTHASE) (DOLICHYL-PHOSPHATE BETA-D- MANNOSYLTRANSFERASE) (MANNOSE-P-DOLICHOL SYNTHASE) (MPD SYNTHASE) (DPM SYNTHASE). [SWISSPROT;Acc:O60762] 1.80836 0.193396779
DPP10 0.031831 2538 DIPEPTIDYLPEPTIDASE 10; DIPEPTIDYL PEPTIDASE IV-RELATED PROTEIN 3. [RefSeq;Acc:NM_020868] 0.148314 0.214618984
DPP6 0.0311751 2539 DIPEPTIDYL AMINOPEPTIDASE-LIKE PROTEIN 6 (DIPEPTIDYLPEPTIDASE VI) (DIPEPTIDYLPEPTIDASE 6) (DIPEPTIDYL PEPTIDASE IV LIKE PROTEIN) (DIPEPTIDYL AMINOPEPTIDASE-RELATED PROTEIN) (DPPX). [SWISSPROT;Acc:P42658] 0.145258 0.214618816
DPP8 0.0310206 2888 DIPEPTIDYL PEPTIDASE 8 ISOFORM 2; DIPEPTIDYL PEPTIDASE 8. [RefSeq;Acc:NM_017743] 0.172385 0.179949532
DPP9 0.0368025 2887 DIPEPTIDYLPEPTIDASE 9; DIPEPTIDYL PEPTIDASE 9; DIPEPTIDYL PEPTIDASE IV-RELATED PROTEIN-2. [RefSeq;Acc:NM_139159] 0.204515 0.179950126
DPY19L1 0.0256791 2118 0.112542 0.228173482
DPY19L2 0.0298356 2112 0.130757 0.228175929
DPY19L2P2 0.0243642 2116 0.106779 0.228174079
DR1 0.263027 30 TATA-BINDING PROTEIN-ASSOCIATED PHOSPHOPROTEIN (DOWN-REGULATOR OF TRANSCRIPTION 1) (DR1 PROTEIN). [SWISSPROT;Acc:Q01658] 0.621928 0.422921946
DRAP1 0.215654 217 DR1-ASSOCIATED PROTEIN 1; NEGATIVE COFACTOR 2 ALPHA; DR1-ASSOCIATED COREPRESSOR. [RefSeq;Acc:NM_006442] 0.675264 0.319362501
DRD4 0.0585879 2509 D(4) DOPAMINE RECEPTOR (D(2C) DOPAMINE RECEPTOR). [SWISSPROT;Acc:P21917] 0.272797 0.214767391
DST 0.0777867 1573 BULLOUS PEMPHIGOID ANTIGEN 1 ISOFORMS 1/2/3/4/5/8 (230 KDA BULLOUS PEMPHIGOID ANTIGEN) (BPA) (HEMIDESMOSOMAL PLAQUE PROTEIN) (DYSTONIA MUSCULORUM PROTEIN) (FRAGMENT). [SWISSPROT;Acc:Q03001] 0.322851 0.240936841
DSTN 0.0460179 371 DESTRIN (ACTIN-DEPOLYMERIZING FACTOR) (ADF). [SWISSPROT;Acc:P18282] 0.164816 0.279207723
DTNA 0.762918 1222 DYSTROBREVIN ALPHA (DYSTROBREVIN-ALPHA). [SWISSPROT;Acc:Q9Y4J8] 3.07607 0.248017113
DTNB 0.86712 1209 DYSTROBREVIN BETA (BETA-DYSTROBREVIN) (DTN-B). [SWISSPROT;Acc:O60941] 3.49509 0.248096616
DTNBP1 0.137665 342 DYSTROBREVIN BINDING PROTEIN 1; DYSBINDIN. [RefSeq;Acc:NM_032122] 0.484315 0.284246823
DTX1 0.177901 147 DELTEX HOMOLOG 1; HDX-1. [RefSeq;Acc:NM_004416] 0.506388 0.351313617
DTX2 0.162688 129 DELTEX 2. [RefSeq;Acc:NM_020892] 0.462821 0.351513868
DTX4 0.205566 156 0.585616 0.351025245
DTYMK 0.51096 1864 THYMIDYLATE KINASE (EC 2.7.4.9) (DTMP KINASE). [SWISSPROT;Acc:P23919] 2.19044 0.233268202
DUS1L 0.155654 215 PP3111 PROTEIN. [RefSeq;Acc:NM_022156] 0.485577 0.320554721
DUT 0.158579 2884 "DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE, MITOCHONDRIAL PRECURSOR (EC 3.6.1.23) (DUTPASE) (DUTP PYROPHOSPHATASE). [SWISSPROT;Acc:P33316]" 0.860412 0.184305891
DVL1 0.217793 761 SEGMENT POLARITY PROTEIN DISHEVELLED HOMOLOG DVL-1 (DISHEVELLED-1) (DSH HOMOLOG 1). [SWISSPROT;Acc:O14640] 0.825859 0.26371693
DVL2 0.223153 762 SEGMENT POLARITY PROTEIN DISHEVELLED HOMOLOG DVL-2 (DISHEVELLED-2) (DSH HOMOLOG 2). [SWISSPROT;Acc:O14641] 0.846393 0.263651755
DVL3 0.256243 771 SEGMENT POLARITY PROTEIN DISHEVELLED HOMOLOG DVL-3 (DISHEVELLED-3) (DSH HOMOLOG 3). [SWISSPROT;Acc:Q92997] 0.973151 0.263312682
DYM 0.50366 558 DYMECLIN. [RefSeq;Acc:NM_017653] 1.85853 0.270999123
DYNC1I1 0.104222 385 "DYNEIN INTERMEDIATE CHAIN 1, CYTOSOLIC (DH IC-1) (CYTOPLASMIC DYNEIN INTERMEDIATE CHAIN 1). [SWISSPROT;Acc:O14576]" 0.373698 0.278893652
DYNC1I2 0.119541 375 "DYNEIN INTERMEDIATE CHAIN 2, CYTOSOLIC (DH IC-2) (CYTOPLASMIC DYNEIN INTERMEDIATE CHAIN 2). [SWISSPROT;Acc:Q13409]" 0.428154 0.279200942
DYNLL2 0.266007 930 DYNEIN LIGHT CHAIN 2. [RefSeq;Acc:NM_080677] 1.03319 0.257461841
DYNLT1 0.587123 3088 CYTOPLASMIC DYNEIN LIGHT CHAIN (T-COMPLEX TESTIS-SPECIFIC PROTEIN 1 HOMOLOG) (PROTEIN CW-1). [SWISSPROT;Acc:Q15763] 6.01339 0.097635942
DYNLT3 0.0365656 3027 T-COMPLEX ASSOCIATED-TESTIS-EXPRESSED 1-LIKE (PROTEIN 91/23). [SWISSPROT;Acc:P51808] 0.307503 0.11891136
DYRK1A 0.135144 348 DUAL-SPECIFICITY TYROSINE-PHOSPHORYLATION REGULATED KINASE 1A (EC 2.7.1.-) (PROTEIN KINASE MINIBRAIN HOMOLOG) (MNBH) (HP86) (DUAL SPECIFICITY YAK1-RELATED KINASE). [SWISSPROT;Acc:Q13627] 0.478436 0.282470383
DYRK1B 0.1052 346 DUAL-SPECIFICITY TYROSINE-PHOSPHORYLATION REGULATED KINASE 1B (EC 2.7.1.-) (MIRK PROTEIN KINASE). [SWISSPROT;Acc:Q9Y463] 0.372425 0.282472981
E2F1 0.198685 82 TRANSCRIPTION FACTOR E2F1 (E2F-1) (RETINOBLASTOMA BINDING PROTEIN 3) (RBBP-3) (PRB-BINDING PROTEIN E2F-1) (PBR3) (RETINOBLASTOMA-ASSOCIATED PROTEIN 1) (RBAP-1). [SWISSPROT;Acc:Q01094] 0.505165 0.393307137
E2F2 0.204365 83 TRANSCRIPTION FACTOR E2F2 (E2F-2). [SWISSPROT;Acc:Q14209] 0.519607 0.393306865
EARS2 0.16091 1444 GLUTAMYL TRNA SYNTHETASE. [SPTREMBL;Acc:O14563] 0.66093 0.243459973
EBNA1BP2 0.271421 1345 PROBABLE RRNA PROCESSING PROTEIN EBP2 (EBNA1 BINDING PROTEIN 2) (NUCLEOLAR PROTEIN P40). [SWISSPROT;Acc:Q99848] 1.10693 0.245201594

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/