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 description measured expected final Hugo
Results: HTML CSV LaTeX Showing element 1858 to 1907 of 3206 in total
Rank
description
measured
expected
final
Hugo
1858 DNA-DIRECTED RNA POLYMERASE II 19 KDA POLYPEPTIDE (EC 2.7.7.6) (RPB7). [SWISSPROT;Acc:P52433] 0.222313 0.952373 0.233430599 POLR2G
1859 0.111248 0.476584 0.233427895 GTPBP8
1860 0.107268 0.459557 0.233416094 POLR3GL
1861 POLYMERASE (RNA) III (DNA DIRECTED) (32KD). [RefSeq;Acc:NM_006467] 0.130061 0.557208 0.233415529 POLR3G
1862 ALANYL-TRNA SYNTHETASE (EC 6.1.1.7) (ALANINE--TRNA LIGASE) (ALARS). [SWISSPROT;Acc:P49588] 0.321507 1.37786 0.23333793 AARS
1863 0.031449 0.134819 0.233268308 DOLK
1864 THYMIDYLATE KINASE (EC 2.7.4.9) (DTMP KINASE). [SWISSPROT;Acc:P23919] 0.51096 2.19044 0.233268202 DTYMK
1865 DYNACTIN 4. [RefSeq;Acc:NM_032486] 0.0462274 0.198227 0.233204357 DCTN5
1866 DIPHOSPHOMEVALONATE DECARBOXYLASE (EC 4.1.1.33) (MEVALONATE PYROPHOSPHATE DECARBOXYLASE) (MEVALONATE (DIPHOSPHO)DECARBOXYLASE). [SWISSPROT;Acc:P53602] 0.0688073 0.295201 0.23308627 MVD
1867 NICOTINATE-NUCLEOTIDE PYROPHOSPHORYLASE [CARBOXYLATING] (EC 2.4.2.19) (QUINOLINATE PHOSPHORIBOSYLTRANSFERASE [DECARBOXYLATING]) (QAPRTASE) (QPRTASE). [SWISSPROT;Acc:Q15274] 0.133589 0.573452 0.232955853 QPRT
1868 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 0.225696 0.232856143 FMO4
1869 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 0.229226 0.232846623 FMO1
1870 "CREATINE KINASE, B CHAIN (EC 2.7.3.2) (B-CK). [SWISSPROT;Acc:P12277]" 0.235164 1.00998 0.232840254 CKB
1871 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 0.232231 0.232837563 FMO2
1872 26S PROTEASE REGULATORY SUBUNIT 4 (P26S4). [SWISSPROT;Acc:Q03527] 0.825694 3.54636 0.23282859 PSMC1
1873 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 0.245601 0.232803205 FMO3
1874 CELLULAR MODULATOR OF IMMUNE RECOGNITION. [RefSeq;Acc:NM_145021] 0.0341996 0.146922 0.232773853 MARCH8
1875 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 0.664457 0.232773528 ACBD3
1876 SARCOGLYCAN ZETA; ZETA-SARCOGLYCAN. [RefSeq;Acc:NM_139167] 0.0628075 0.269823 0.232772966 SGCZ
1877 GAMMA-SARCOGLYCAN (GAMMA-SG) (35 KDA DYSTROPHIN-ASSOCIATED GLYCOPROTEIN) (35DAG). [SWISSPROT;Acc:Q13326] 0.0566858 0.243524 0.232772951 SGCG
1878 DELTA-SARCOGLYCAN (SG-DELTA) (35 KDA DYSTROPHIN-ASSOCIATED GLYCOPROTEIN) (35DAG). [SWISSPROT;Acc:Q92629] 0.0630725 0.270962 0.232772492 SGCD
1879 VACUOLAR ATP SYNTHASE 21 KDA PROTEOLIPID SUBUNIT (EC 3.6.3.14) (HATPL). [SWISSPROT;Acc:Q99437] 0.465943 2.00171 0.23277248 ATP6V0B
1880 VACUOLAR ATP SYNTHASE 16 KDA PROTEOLIPID SUBUNIT (EC 3.6.3.14). [SWISSPROT;Acc:P27449] 0.556589 2.39113 0.232772371 ATP6V0C
1881 0.0285481 0.122644 0.232772088 MARCH1
1882 "CREATINE KINASE, UBIQUITOUS MITOCHONDRIAL PRECURSOR (EC 2.7.3.2) (U- MTCK) (MIA-CK) (ACIDIC-TYPE MITOCHONDRIAL CREATINE KINASE). [SWISSPROT;Acc:P12532]" 0.199469 0.856983 0.232757243 no value
1883 "CREATINE KINASE, SARCOMERIC MITOCHONDRIAL PRECURSOR (EC 2.7.3.2) (S- MTCK) (MIB-CK) (BASIC-TYPE MITOCHONDRIAL CREATINE KINASE). [SWISSPROT;Acc:P17540]" 0.197547 0.848743 0.232752435 CKMT2
1884 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 0.269788 0.232748677 FMO6P
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 J DOMAIN PROTEIN C21ORF55. [SWISSPROT;Acc:Q9NX36] 0.107843 0.463351 0.232745802 C21orf55
1887 PEPTIDYL PROLYL ISOMERASE H; CYCLOPHILIN H. [RefSeq;Acc:NM_006347] 0.039427 0.1694 0.232744982 PPIH
1888 PRP18 PRE-MRNA PROCESSING FACTOR 18 HOMOLOG. [RefSeq;Acc:NM_003675] 0.184055 0.790803 0.232744438 PRPF18
1889 DIHYDROFOLATE REDUCTASE (EC 1.5.1.3). [SWISSPROT;Acc:P00374] 0.241532 1.03785 0.232723419 no value
1890 STROMAL CELL-DERIVED FACTOR 2-LIKE PROTEIN 1 PRECURSOR (SDF2 LIKE PROTEIN 1) (PWP1-INTERACTING PROTEIN 8). [SWISSPROT;Acc:Q9HCN8] 0.0221128 0.0950179 0.232722466 SDF2L1
1891 STROMAL CELL-DERIVED FACTOR 2 PRECURSOR (SDF-2). [SWISSPROT;Acc:Q99470] 0.0275634 0.118439 0.23272233 SDF2
1892 THYMIDYLATE SYNTHASE (EC 2.1.1.45) (TS) (TSASE). [SWISSPROT;Acc:P04818] TYMS
1893 60S RIBOSOMAL PROTEIN L3-LIKE. [SWISSPROT;Acc:Q92901] 1.34083 5.76236 0.232687649 RPL3L
1894 "CREATINE KINASE, M CHAIN (EC 2.7.3.2) (M-CK). [SWISSPROT;Acc:P06732]" 0.219925 0.945419 0.232621726 CKM
1895 MICROTUBULE-ASSOCIATED PROTEIN 4 (MAP 4). [SWISSPROT;Acc:P27816] 0.036083 0.155117 0.232617959 MAP4
1896 VAM6/VPS39-LIKE PROTEIN (HVAM6P). [SWISSPROT;Acc:Q96JC1] 0.403209 1.73336 0.232616998 VPS39
1897 40S RIBOSOMAL PROTEIN S13. [SWISSPROT;Acc:Q02546] 0.3472 1.49288 0.232570602 RPS13
1898 "TRANSLATION INITIATION FACTOR IF-2, MITOCHONDRIAL PRECURSOR (IF-2MT) (IF-2(MT)). [SWISSPROT;Acc:P46199]" 0.416108 1.78993 0.232471661 MTIF2
1899 60S RIBOSOMAL PROTEIN L17 (L23). [SWISSPROT;Acc:P18621] 0.63284 2.72242 0.232454948 no value
1900 ENDOTHELIAL-DERIVED GENE 1. [RefSeq;Acc:NM_025205] 0.0600275 0.258242 0.232446697 MED28
1901 RRP5 PROTEIN HOMOLOG (PROGRAMMED CELL DEATH PROTEIN 11). [SWISSPROT;Acc:Q14690] 0.132484 0.570026 0.232417469 PDCD11
1902 0.549308 2.36366 0.232397214 no value
1903 "SERINE HYDROXYMETHYLTRANSFERASE, MITOCHONDRIAL PRECURSOR (EC 2.1.2.1) (SERINE METHYLASE) (GLYCINE HYDROXYMETHYLTRANSFERASE) (SHMT). [SWISSPROT;Acc:P34897]" 0.413255 1.77935 0.232250541 SHMT2
1904 DNA-DIRECTED RNA POLYMERASE II 23 KDA POLYPEPTIDE (EC 2.7.7.6) (RPB25) (XAP4) (RPB5) (RPABC1). [SWISSPROT;Acc:P19388] 0.465033 2.00245 0.232232016 POLR2E
1905 "UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT, MITOCHONDRIAL PRECURSOR (EC 1.10.2.2) (RIESKE IRON-SULFUR PROTEIN) (RISP). [SWISSPROT;Acc:P47985]" 0.102272 0.440396 0.232227359 UQCRFSL1
1906 SUPPRESSOR OF TY 5 HOMOLOG; SUPPRESSOR OF TY (S.CEREVISIAE) 5 HOMOLOG. [RefSeq;Acc:NM_003169] 1.04135 4.48455 0.23220836 no value
1907 0.0196837 0.0847765 0.232183447 LTV1

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/