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 Hugo Rank measured description expected final
Results: HTML CSV LaTeX Showing element 2208 to 2257 of 3206 in total
Hugo
Rank
measured
description
expected
final
PMP2 288 0.0373888 MYELIN P2 PROTEIN. [SWISSPROT;Acc:P02689] 0.123882 0.301809787
PMPCA 2499 0.235517 "MITOCHONDRIAL PROCESSING PEPTIDASE ALPHA SUBUNIT, MITOCHONDRIAL PRECURSOR (EC 3.4.24.64) (ALPHA-MPP) (P-55) (HA1523). [SWISSPROT;Acc:Q10713]" 1.09378 0.215323923
PMPCB 2500 0.208649 "MITOCHONDRIAL PROCESSING PEPTIDASE BETA SUBUNIT, MITOCHONDRIAL PRECURSOR (EC 3.4.24.64) (BETA-MPP) (P-52). [SWISSPROT;Acc:O75439]" 0.969013 0.215321157
PMS2 2226 0.145091 PMS1 PROTEIN HOMOLOG 2 (DNA MISMATCH REPAIR PROTEIN PMS2). [SWISSPROT;Acc:P54278] 0.6464 0.224460087
PNKD 2587 0.48801 MYOFIBRILLOGENESIS REGULATOR 1; TRANS-ACTIVATED BY HEPATITIS C VIRUS CORE PROTEIN 2; LIKELY ORTHOLOG OF MOUSE BRAIN PROTEIN 17. [RefSeq;Acc:NM_022572] 2.292 0.212918848
PNMT 293 0.0437393 PHENYLETHANOLAMINE N-METHYLTRANSFERASE (EC 2.1.1.28) (PNMTASE) (NORADRENALINE N-METHYLTRANSFERASE). [SWISSPROT;Acc:P11086] 0.144924 0.301808534
PNN 2214 0.168935 "PININ, DESMOSOME ASSOCIATED PROTEIN; PININ. [RefSeq;Acc:NM_002687]" 0.750817 0.225001565
PNO1 1010 0.222495 PUTATATIVE 28 KDA PROTEIN. [RefSeq;Acc:NM_020143] 0.87407 0.254550551
PNPLA7 1711 0.18248 0.768033 0.237593958
PNPO 1131 0.0418316 PYRIDOXINE 5'-PHOSPHATE OXIDASE. [RefSeq;Acc:NM_018129] 0.166987 0.250508123
POLDIP2 1976 0.0281946 DNA POLYMERASE DELTA P38 SUBUNIT. [RefSeq;Acc:NM_015584] 0.122012 0.231080549
POLE 235 0.259541 "DNA POLYMERASE EPSILON, CATALYTIC SUBUNIT A (EC 2.7.7.7) (DNA POLYMERASE II SUBUNIT A). [SWISSPROT;Acc:Q07864]" 0.824492 0.314788985
POLE2 110 0.0886771 DNA POLYMERASE EPSILON SUBUNIT B (EC 2.7.7.7) (DNA POLYMERASE II SUBUNIT B). [SWISSPROT;Acc:P56282] 0.24446 0.362746871
POLE3 65 0.446035 DNA POLYMERASE EPSILON P17 SUBUNIT (DNA POLYMERASE EPSILON SUBUNIT 3) (CHROMATIN ACCESSIBILITY COMPLEX 17) (HUCHRAC17) (CHRAC-17). [SWISSPROT;Acc:Q9NRF9] 1.09489 0.407378823
POLE4 9 0.803534 DNA POLYMERASE EPSILON P12 SUBUNIT (DNA POLYMERASE EPSILON SUBUNIT 4). [SWISSPROT;Acc:Q9NR33] 1.40271 0.572843995
POLG 2311 0.0274568 DNA POLYMERASE GAMMA SUBUNIT 1 (EC 2.7.7.7) (MITOCHONDRIAL DNA POLYMERASE CATALYTIC SUBUNIT) (POLG-ALPHA). [SWISSPROT;Acc:P54098] 0.123653 0.22204718
POLI 197 0.048504 "POLYMERASE (DNA DIRECTED) IOTA; RAD30 (S. CEREVISIAE) HOMOLOG B; POLYMERASE (DNA-DIRECTED), IOTA. [RefSeq;Acc:NM_007195]" 0.150395 0.322510722
POLR1A 1983 0.661854 DNA-DIRECTED RNA POLYMERASE I LARGEST SUBUNIT (EC 2.7.7.6) (RNA POLYMERASE I 194 KDA SUBUNIT) (RPA194). [SWISSPROT;Acc:O95602] 2.86554 0.230970079
POLR1B 1951 0.820741 DNA-DIRECTED RNA POLYMERASE I 135 KDA POLYPEPTIDE (EC 2.7.7.6) (RNA POLYMERASE I SUBUNIT 2) (RPA135). [SWISSPROT;Acc:Q9H9Y6] 3.54858 0.231287163
POLR1C 2046 1.55851 DNA-DIRECTED RNA POLYMERASE I 40 KDA POLYPEPTIDE (EC 2.7.7.6) (RPA40) (RPA39). [SWISSPROT;Acc:O15160] 6.77601 0.230004088
POLR1E 1972 0.0824177 RNA POLYMERASE I ASSOCIATED FACTOR 53. [RefSeq;Acc:NM_022490] 0.356578 0.231135123
POLR2A 1990 0.525129 DNA-DIRECTED RNA POLYMERASE II LARGEST SUBUNIT (EC 2.7.7.6) (RPB1). [SWISSPROT;Acc:P24928] 2.27455 0.230871601
POLR2B 1939 0.593881 DNA-DIRECTED RNA POLYMERASE II 140 KDA POLYPEPTIDE (EC 2.7.7.6) (RNA POLYMERASE II SUBUNIT 2) (RPB2). [SWISSPROT;Acc:P30876] 2.5639 0.231631889
POLR2C 2070 1.60424 DNA-DIRECTED RNA POLYMERASE II 33 KDA POLYPEPTIDE (EC 2.7.7.6) (RPB3) (RNA POLYMERASE II SUBUNIT 3) (RPB33) (RPB31). [SWISSPROT;Acc:P19387] 6.99164 0.229451173
POLR2D 1246 0.139566 DNA-DIRECTED RNA POLYMERASE II 16 KDA POLYPEPTIDE (EC 2.7.7.6) (RPB4). [SWISSPROT;Acc:O15514] 0.563754 0.247565427
POLR2E 1904 0.465033 DNA-DIRECTED RNA POLYMERASE II 23 KDA POLYPEPTIDE (EC 2.7.7.6) (RPB25) (XAP4) (RPB5) (RPABC1). [SWISSPROT;Acc:P19388] 2.00245 0.232232016
POLR2F 2282 0.848404 DNA-DIRECTED RNA POLYMERASE II 14.4 KDA POLYPEPTIDE (EC 2.7.7.6) (RPB6) (RPB14.4) (RPABC2). [SWISSPROT;Acc:P41584] 3.81401 0.222444094
POLR2G 1858 0.222313 DNA-DIRECTED RNA POLYMERASE II 19 KDA POLYPEPTIDE (EC 2.7.7.6) (RPB7). [SWISSPROT;Acc:P52433] 0.952373 0.233430599
POLR2H 1541 0.345751 "DNA-DIRECTED RNA POLYMERASES I, II, AND III 17.1 KDA POLYPEPTIDE (EC 2.7.7.6) (RPB17) (RPB8) (RPABC3). [SWISSPROT;Acc:P52434]" 1.42971 0.241832959
POLR2I 2044 0.110371 DNA-DIRECTED RNA POLYMERASE II 14.5 KDA POLYPEPTIDE (EC 2.7.7.6) (RPB9) (RPB14.5). [SWISSPROT;Acc:P36954] 0.479632 0.230116006
POLR2J 2285 0.249308 DNA-DIRECTED RNA POLYMERASE II 13.3 KDA POLYPEPTIDE (EC 2.7.7.6) (RPB11). [SWISSPROT;Acc:P52435] 1.12113 0.222372071
POLR2L 1835 0.508074 DNA-DIRECTED RNA POLYMERASE II 7.6 KDA POLYPEPTIDE (EC 2.7.7.6) (RPB10) (RPB7.6) (RPABC5). [SWISSPROT;Acc:P52436] 2.17246 0.233870359
POLR3A 1969 0.677997 DNA-DIRECTED RNA POLYMERASE III LARGEST SUBUNIT (EC 2.7.7.6) (RPC155) (RPC1). [SWISSPROT;Acc:O14802] 2.9329 0.231169491
POLR3C 1924 0.192198 POLYMERASE (RNA) III (DNA DIRECTED) (62KD). [RefSeq;Acc:NM_006468] 0.828592 0.231957345
POLR3F 1914 0.171101 DNA-DIRECTED RNA POLYMERASES III 39 KDA POLYPEPTIDE (EC 2.7.7.6) (RNA POLYMERASE III C39 SUBUNIT). [SWISSPROT;Acc:Q9H1D9] 0.737404 0.232031559
POLR3G 1861 0.130061 POLYMERASE (RNA) III (DNA DIRECTED) (32KD). [RefSeq;Acc:NM_006467] 0.557208 0.233415529
POLR3GL 1860 0.107268 0.459557 0.233416094
POLR3K 1791 0.163024 DNA-DIRECTED RNA POLYMERASES III 12.5 KDA POLYPEPTIDE (EC 2.7.7.6) (RNA POLYMERASE III C11 SUBUNIT) (HSC11P) (HRPC11) (MY010 PROTEIN). [SWISSPROT;Acc:Q9Y2Y1] 0.693873 0.234947894
POLS 2267 0.0673124 POLYMERASE (DNA DIRECTED) SIGMA; TOPOISOMERASE-RELATED FUNCTION PROTEIN 4-1; POLYMERASE (DNA-DIRECTED) SIGMA. [RefSeq;Acc:NM_006999] 0.302153 0.222775878
POR 1917 0.0187206 NADPH-CYTOCHROME P450 REDUCTASE (EC 1.6.2.4) (CPR) (P450R). [SWISSPROT;Acc:P16435] 0.0807026 0.231970222
PPA1 2049 0.128098 INORGANIC PYROPHOSPHATASE (EC 3.6.1.1) (PYROPHOSPHATE PHOSPHO- HYDROLASE) (PPASE). [SWISSPROT;Acc:Q15181] 0.557073 0.229948319
PPA2 2047 0.123888 INORGANIC PYROPHOSPHATASE 2 ISOFORM 1. [RefSeq;Acc:NM_176869] 0.538763 0.229948976
PPAN-P2RY11 1335 0.0742746 SUPPRESSOR OF SWI4 1 HOMOLOG (SSF-1) (PETER PAN HOMOLOG). [SWISSPROT;Acc:Q9NQ55] 0.302799 0.245293412
PPAT 1687 0.214575 AMIDOPHOSPHORIBOSYLTRANSFERASE PRECURSOR (EC 2.4.2.14) (GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE AMIDOTRANSFERASE) (ATASE) (GPAT). [SWISSPROT;Acc:Q06203] 0.901215 0.238095238
PPCDC 2744 0.111176 0.543616 0.204512008
PPCS 2745 0.0833819 0.407712 0.204511763
PPIB 2100 0.0360136 PEPTIDYL-PROLYL CIS-TRANS ISOMERASE B PRECURSOR (EC 5.2.1.8) (PPIASE) (ROTAMASE) (CYCLOPHILIN B) (S-CYCLOPHILIN) (SCYLP) (CYP-S1). [SWISSPROT;Acc:P23284] 0.15771 0.228353307
PPIE 3018 0.0424091 PEPTIDYL-PROLYL CIS-TRANS ISOMERASE E (EC 5.2.1.8) (PPIASE E) (ROTAMASE E) (CYCLOPHILIN E) (CYCLOPHILIN 33). [SWISSPROT;Acc:Q9UNP9] 0.349357 0.121391871
PPIH 1887 0.039427 PEPTIDYL PROLYL ISOMERASE H; CYCLOPHILIN H. [RefSeq;Acc:NM_006347] 0.1694 0.232744982
PPIL4 904 0.227308 PEPTIDYLPROLYL ISOMERASE-LIKE 4; CYCLOPHILIN-TYPE PEPTIDYL-PROLYL CIS-TRANS ISOMERASE; PPIASE; SEROLOGICALLY DEFINED BREAST CANCER ANTIGEN NY-BR-18. [RefSeq;Acc:NM_139126] 0.879442 0.258468438

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/