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 expected description measured Hugo final
Results: HTML CSV LaTeX Showing element 1852 to 1901 of 3206 in total
Rank
expected
description
measured
Hugo
final
1852 0.142049 PRESENILIN-LIKE PROTEIN 1 (EC 3.4.99.-) (SPPL2B PROTEIN). [SWISSPROT;Acc:Q8TCT7] 0.0331615 no value 0.233451133
1853
1854 0.117581 0.0274494 0.233450983
1855 0.117865 PRESENILIN-LIKE PROTEIN 2 (EC 3.4.99.-) (SPPL2A PROTEIN). [SWISSPROT;Acc:Q8TCT8] 0.0275157 0.233450982
1856 2.00865 GTP-BINDING NUCLEAR PROTEIN RAN (TC4) (RAN GTPASE) (ANDROGEN RECEPTOR- ASSOCIATED PROTEIN 24). [SWISSPROT;Acc:P17080] 0.46892 RANP1 0.233450327
1857 0.108089 0.0252313 FCF1 0.233430784
1858 0.952373 DNA-DIRECTED RNA POLYMERASE II 19 KDA POLYPEPTIDE (EC 2.7.7.6) (RPB7). [SWISSPROT;Acc:P52433] 0.222313 POLR2G 0.233430599
1859 0.476584 0.111248 GTPBP8 0.233427895
1860 0.459557 0.107268 POLR3GL 0.233416094
1861 0.557208 POLYMERASE (RNA) III (DNA DIRECTED) (32KD). [RefSeq;Acc:NM_006467] 0.130061 POLR3G 0.233415529
1862 1.37786 ALANYL-TRNA SYNTHETASE (EC 6.1.1.7) (ALANINE--TRNA LIGASE) (ALARS). [SWISSPROT;Acc:P49588] 0.321507 AARS 0.23333793
1863 0.134819 0.031449 DOLK 0.233268308
1864 2.19044 THYMIDYLATE KINASE (EC 2.7.4.9) (DTMP KINASE). [SWISSPROT;Acc:P23919] 0.51096 DTYMK 0.233268202
1865 0.198227 DYNACTIN 4. [RefSeq;Acc:NM_032486] 0.0462274 DCTN5 0.233204357
1866 0.295201 DIPHOSPHOMEVALONATE DECARBOXYLASE (EC 4.1.1.33) (MEVALONATE PYROPHOSPHATE DECARBOXYLASE) (MEVALONATE (DIPHOSPHO)DECARBOXYLASE). [SWISSPROT;Acc:P53602] 0.0688073 MVD 0.23308627
1867 0.573452 NICOTINATE-NUCLEOTIDE PYROPHOSPHORYLASE [CARBOXYLATING] (EC 2.4.2.19) (QUINOLINATE PHOSPHORIBOSYLTRANSFERASE [DECARBOXYLATING]) (QAPRTASE) (QPRTASE). [SWISSPROT;Acc:Q15274] 0.133589 QPRT 0.232955853
1868 0.225696 DIMETHYLANILINE MONOOXYGENASE [N-OXIDE FORMING] 4 (EC 1.14.13.8) (HEPATIC FLAVIN-CONTAINING MONOOXYGENASE 4) (FMO 4) (DIMETHYLANILINE OXIDASE 4). [SWISSPROT;Acc:P31512] 0.0525547 FMO4 0.232856143
1869 0.229226 DIMETHYLANILINE MONOOXYGENASE [N-OXIDE FORMING] 1 (EC 1.14.13.8) (FETAL HEPATIC FLAVIN-CONTAINING MONOOXYGENASE 1) (FMO 1) (DIMETHYLANILINE OXIDASE 1). [SWISSPROT;Acc:Q01740] 0.0533745 FMO1 0.232846623
1870 1.00998 "CREATINE KINASE, B CHAIN (EC 2.7.3.2) (B-CK). [SWISSPROT;Acc:P12277]" 0.235164 CKB 0.232840254
1871 0.232231 DIMETHYLANILINE MONOOXYGENASE [N-OXIDE FORMING] 2 (EC 1.14.13.8) (PULMONARY FLAVIN-CONTAINING MONOOXYGENASE 2) (FMO 2) (DIMETHYLANILINE OXIDASE 2) (FMO 1B1). [SWISSPROT;Acc:Q99518] 0.0540721 FMO2 0.232837563
1872 3.54636 26S PROTEASE REGULATORY SUBUNIT 4 (P26S4). [SWISSPROT;Acc:Q03527] 0.825694 PSMC1 0.23282859
1873 0.245601 DIMETHYLANILINE MONOOXYGENASE [N-OXIDE FORMING] 3 (EC 1.14.13.8) (HEPATIC FLAVIN-CONTAINING MONOOXYGENASE 3) (FMO 3) (DIMETHYLANILINE OXIDASE 3) (FMO FORM 2) (FMO II). [SWISSPROT;Acc:P31513] 0.0571767 FMO3 0.232803205
1874 0.146922 CELLULAR MODULATOR OF IMMUNE RECOGNITION. [RefSeq;Acc:NM_145021] 0.0341996 MARCH8 0.232773853
1875 0.664457 GOLGI COMPLEX ASSOCIATED PROTEIN 1; GOLGI RESIDENT PROTEIN GCP60; PERIPHERIAL BENZODIAZEPINE RECEPTOR ASSOCIATED PROTEIN; GOLGI PHOSPHOPROTEIN 1; PBR ASSOCIATED PROTEIN; PKA (RIALPHA)-ASSOCIATED PROTEIN. [RefSeq;Acc:NM_022735] 0.154668 ACBD3 0.232773528
1876 0.269823 SARCOGLYCAN ZETA; ZETA-SARCOGLYCAN. [RefSeq;Acc:NM_139167] 0.0628075 SGCZ 0.232772966
1877 0.243524 GAMMA-SARCOGLYCAN (GAMMA-SG) (35 KDA DYSTROPHIN-ASSOCIATED GLYCOPROTEIN) (35DAG). [SWISSPROT;Acc:Q13326] 0.0566858 SGCG 0.232772951
1878 0.270962 DELTA-SARCOGLYCAN (SG-DELTA) (35 KDA DYSTROPHIN-ASSOCIATED GLYCOPROTEIN) (35DAG). [SWISSPROT;Acc:Q92629] 0.0630725 SGCD 0.232772492
1879 2.00171 VACUOLAR ATP SYNTHASE 21 KDA PROTEOLIPID SUBUNIT (EC 3.6.3.14) (HATPL). [SWISSPROT;Acc:Q99437] 0.465943 ATP6V0B 0.23277248
1880 2.39113 VACUOLAR ATP SYNTHASE 16 KDA PROTEOLIPID SUBUNIT (EC 3.6.3.14). [SWISSPROT;Acc:P27449] 0.556589 ATP6V0C 0.232772371
1881 0.122644 0.0285481 MARCH1 0.232772088
1882 0.856983 "CREATINE KINASE, UBIQUITOUS MITOCHONDRIAL PRECURSOR (EC 2.7.3.2) (U- MTCK) (MIA-CK) (ACIDIC-TYPE MITOCHONDRIAL CREATINE KINASE). [SWISSPROT;Acc:P12532]" 0.199469 no value 0.232757243
1883 0.848743 "CREATINE KINASE, SARCOMERIC MITOCHONDRIAL PRECURSOR (EC 2.7.3.2) (S- MTCK) (MIB-CK) (BASIC-TYPE MITOCHONDRIAL CREATINE KINASE). [SWISSPROT;Acc:P17540]" 0.197547 CKMT2 0.232752435
1884 0.269788 PUTATIVE DIMETHYLANILINE MONOOXYGENASE [N-OXIDE FORMING] 6 (EC 1.14.13.8) (FLAVIN-CONTAINING MONOOXYGENASE 6) (FMO 6) (DIMETHYLANILINE OXIDASE 6). [SWISSPROT;Acc:O60774] 0.0627928 FMO6P 0.232748677
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] FMO5
1886 0.463351 J DOMAIN PROTEIN C21ORF55. [SWISSPROT;Acc:Q9NX36] 0.107843 C21orf55 0.232745802
1887 0.1694 PEPTIDYL PROLYL ISOMERASE H; CYCLOPHILIN H. [RefSeq;Acc:NM_006347] 0.039427 PPIH 0.232744982
1888 0.790803 PRP18 PRE-MRNA PROCESSING FACTOR 18 HOMOLOG. [RefSeq;Acc:NM_003675] 0.184055 PRPF18 0.232744438
1889 1.03785 DIHYDROFOLATE REDUCTASE (EC 1.5.1.3). [SWISSPROT;Acc:P00374] 0.241532 no value 0.232723419
1890 0.0950179 STROMAL CELL-DERIVED FACTOR 2-LIKE PROTEIN 1 PRECURSOR (SDF2 LIKE PROTEIN 1) (PWP1-INTERACTING PROTEIN 8). [SWISSPROT;Acc:Q9HCN8] 0.0221128 SDF2L1 0.232722466
1891 0.118439 STROMAL CELL-DERIVED FACTOR 2 PRECURSOR (SDF-2). [SWISSPROT;Acc:Q99470] 0.0275634 SDF2 0.23272233
1892 THYMIDYLATE SYNTHASE (EC 2.1.1.45) (TS) (TSASE). [SWISSPROT;Acc:P04818] TYMS
1893 5.76236 60S RIBOSOMAL PROTEIN L3-LIKE. [SWISSPROT;Acc:Q92901] 1.34083 RPL3L 0.232687649
1894 0.945419 "CREATINE KINASE, M CHAIN (EC 2.7.3.2) (M-CK). [SWISSPROT;Acc:P06732]" 0.219925 CKM 0.232621726
1895 0.155117 MICROTUBULE-ASSOCIATED PROTEIN 4 (MAP 4). [SWISSPROT;Acc:P27816] 0.036083 MAP4 0.232617959
1896 1.73336 VAM6/VPS39-LIKE PROTEIN (HVAM6P). [SWISSPROT;Acc:Q96JC1] 0.403209 VPS39 0.232616998
1897 1.49288 40S RIBOSOMAL PROTEIN S13. [SWISSPROT;Acc:Q02546] 0.3472 RPS13 0.232570602
1898 1.78993 "TRANSLATION INITIATION FACTOR IF-2, MITOCHONDRIAL PRECURSOR (IF-2MT) (IF-2(MT)). [SWISSPROT;Acc:P46199]" 0.416108 MTIF2 0.232471661
1899 2.72242 60S RIBOSOMAL PROTEIN L17 (L23). [SWISSPROT;Acc:P18621] 0.63284 no value 0.232454948
1900 0.258242 ENDOTHELIAL-DERIVED GENE 1. [RefSeq;Acc:NM_025205] 0.0600275 MED28 0.232446697
1901 0.570026 RRP5 PROTEIN HOMOLOG (PROGRAMMED CELL DEATH PROTEIN 11). [SWISSPROT;Acc:Q14690] 0.132484 PDCD11 0.232417469

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/