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.


Navigation/Query Panel:
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Gene Rank expected description measured Hugo final
Results: HTML CSV LaTeX Showing element 1802 to 1851 of 3206 in total
Rank
expected
description
measured
Hugo
final
1802 0.233549 RAN BINDING PROTEIN 11. [RefSeq;Acc:NM_016338] 0.0547985 IPO11 0.234633846
1803 1.0482 HEPATOCYTE GROWTH FACTOR-REGULATED TYROSINE KINASE SUBSTRATE; HUMAN GROWTH FACTOR-REGULATED TYROSINE KINASE SUBSTRATE. [RefSeq;Acc:NM_004712] 0.24593 HGS 0.234621255
1804 0.153963 CONSERVED OLIGOMERIC GOLGI COMPLEX COMPONENT 7. [SWISSPROT;Acc:P83436] 0.0361228 COG7 0.234620006
1805 1.06873 GTP CYCLOHYDROLASE I (EC 3.5.4.16) (GTP-CH-I). [SWISSPROT;Acc:P30793] 0.250702 GCH1 0.234579361
1806 0.562339 P53-RELATED PROTEIN KINASE (EC 2.7.1.-) (NORI-2). [SWISSPROT;Acc:Q96S44] 0.131908 TP53RK 0.23457025
1807 0.165025 "EARLY ENDOSOME ANTIGEN 1, 162KD; EARLY ENDOSOME-ASSOCIATED PROTEIN. [RefSeq;Acc:NM_003566]" 0.0387072 EEA1 0.234553552
1808 0.623804 0.146293 MED9 0.234517573
1809 0.0715398 CARBOXYPEPTIDASE A5. [RefSeq;Acc:NM_080385] 0.0167711 CPA5 0.234430345
1810 0.0912429 CARBOXYPEPTIDASE A1 PRECURSOR (EC 3.4.17.1). [SWISSPROT;Acc:P15085] 0.0213901 CPA1 0.234430295
1811 0.773023 AMINOACYLASE-1 (EC 3.5.1.14) (N-ACYL-L-AMINO-ACID AMIDOHYDROLASE) (ACY-1). [SWISSPROT;Acc:Q03154] 0.18122 ACY1 0.234430282
1812 0.0914656 "NEUTRAL AND BASIC AMINO ACID TRANSPORT PROTEIN RBAT (B(0,+)-TYPE AMINO ACID TRANSPORT PROTEIN) (NBAT) (D2H). [SWISSPROT;Acc:Q07837]" 0.0214423 SLC3A1 0.234430212
1813 0.059666 CARBOXYPEPTIDASE B PRECURSOR (EC 3.4.17.2) (PANCREAS-SPECIFIC PROTEIN) (PASP). [SWISSPROT;Acc:P15086] 0.0139875 CPB1 0.234429994
1814 3.36493 60S RIBOSOMAL PROTEIN L9. [SWISSPROT;Acc:P32969] 0.788679 no value 0.234381993
1815 3.09996 PROTEASOME SUBUNIT ALPHA TYPE 7-LIKE (EC 3.4.25.1). [SWISSPROT;Acc:Q8TAA3] 0.726532 PSMA8 0.234368185
1816 0.783008 UNC-119 PROTEIN HOMOLOG (RETINAL PROTEIN 4) (HRG4). [SWISSPROT;Acc:Q13432] 0.183433 UNC119 0.234267083
1817 0.326253 DNA FRAGMENTATION FACTOR ALPHA SUBUNIT (DNA FRAGMENTATION FACTOR 45 KDA SUBUNIT) (DFF-45) (INHIBITOR OF CAD) (ICAD). [SWISSPROT;Acc:O00273] 0.0764303 DFFA 0.234266965
1818 0.128045 ANKYRIN 3 (ANK-3) (ANKYRIN G). [SWISSPROT;Acc:Q12955] 0.0299967 ANK3 0.234266859
1819 0.326867 ADAMTS-9 PRECURSOR (EC 3.4.24.-) (A DISINTEGRIN AND METALLOPROTEINASE WITH THROMBOSPONDIN MOTIFS 9) (ADAM-TS 9) (ADAM-TS9). [SWISSPROT;Acc:Q9P2N4] 0.0765741 ADAMTS9 0.234266842
1820 3.51793 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 8 (26S PROTEASOME REGULATORY SUBUNIT S14) (P31). [SWISSPROT;Acc:P48556] 0.824134 PSMD8 0.234266742
1821 0.654349 DNA FRAGMENTATION FACTOR 40 KDA SUBUNIT (EC 3.-.-.-) (DFF-40) (CASPASE-ACTIVATED DEOXYRIBONUCLEASE) (CASPASE-ACTIVATED DNASE) (CAD) (CASPASE-ACTIVATED NUCLEASE) (CPAN). [SWISSPROT;Acc:O76075] 0.153292 DFFB 0.234266424
1822 0.163741 ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 3. [SWISSPROT;Acc:P36405] 0.038359 ARL3 0.234266311
1823 no value
1824 "ANKYRIN 2 (BRAIN ANKYRIN) (ANKYRIN B) (ANKYRIN, NONERYTHROID). [SWISSPROT;Acc:Q01484]" ANK2
1825 1.45621 0.341137 RFK 0.234263602
1826 3.47138 PROTEASOME SUBUNIT ALPHA TYPE 7 (EC 3.4.25.1) (PROTEASOME SUBUNIT RC6-1) (PROTEASOME SUBUNIT XAPC7). [SWISSPROT;Acc:O14818] 0.813157 PSMA7 0.234246035
1827 2.20733 "SERINE/THREONINE PROTEIN PHOSPHATASE 2A, CATALYTIC SUBUNIT, ALPHA ISOFORM (EC 3.1.3.16) (PP2A-ALPHA) (REPLICATION PROTEIN C) (RP-C). [SWISSPROT;Acc:P05323]" 0.517007 PPP2CA 0.234222794
1828 2.28647 S-ADENOSYLMETHIONINE SYNTHETASE ALPHA AND BETA FORMS (EC 2.5.1.6) (METHIONINE ADENOSYLTRANSFERASE) (ADOMET SYNTHETASE) (MAT-I/III). [SWISSPROT;Acc:Q00266] 0.53545 MAT1A 0.234181949
1829 0.0954818 APOPAIN PRECURSOR (EC 3.4.22.-) (CYSTEINE PROTEASE CPP32) (YAMA PROTEIN) (CPP-32) (CASPASE-3) (CASP-3) (SREBP CLEAVAGE ACTIVITY 1) (SCA-1). [SWISSPROT;Acc:P42574] 0.0223509 CASP3 0.234085449
1830 0.120482 CASPASE-7 PRECURSOR (EC 3.4.22.-) (ICE-LIKE APOPTOTIC PROTEASE 3) (ICE-LAP3) (APOPTOTIC PROTEASE MCH-3) (CMH-1). [SWISSPROT;Acc:P55210] 0.028203 CASP7 0.23408476
1831 1.12425 0.263169 TSR1 0.234084056
1832 0.233559 VALYL-TRNA SYNTHETASE 2 (EC 6.1.1.9) (VALINE--TRNA LIGASE 2) (VALRS 2) (G7A). [SWISSPROT;Acc:P26640] 0.0546688 VARS 0.234068479
1833 0.43244 N-ACETYLTRANSFERASE 5 (EC 2.3.1.-). [SWISSPROT;Acc:Q9Y6D2] 0.101148 NAT5 0.233900657
1834 0.827963 RIBOSOMAL PROTEIN L24-LIKE; 60S RIBOSOMAL PROTEIN L30 ISOLOG; MY024 PROTEIN; HOMOLOG OF YEAST RIBOSOMAL LIKE PROTEIN 24. [RefSeq;Acc:NM_016304] 0.193647 C15orf15 0.23388364
1835 2.17246 DNA-DIRECTED RNA POLYMERASE II 7.6 KDA POLYPEPTIDE (EC 2.7.7.6) (RPB10) (RPB7.6) (RPABC5). [SWISSPROT;Acc:P52436] 0.508074 POLR2L 0.233870359
1836 1.32969 U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM1 (SMALL NUCLEAR RIBONUCLEAR CASM) (CANCER-ASSOCIATED SM-LIKE). [SWISSPROT;Acc:O15116] 0.31086 LSM1 0.233783814
1837 0.327833 0.0766245 C8orf53 0.233730283
1838 0.38998 0.0910964 MTHFD1L 0.233592492
1839 0.780167 40S RIBOSOMAL PROTEIN S24 (S19). [SWISSPROT;Acc:P16632] 0.182207 RPS24 0.233548715
1840 0.114733 0.0267948 C18orf22 0.233540481
1841 0.803133 60S RIBOSOMAL PROTEIN L39. [SWISSPROT;Acc:P02404] 0.187564 no value 0.233540397
1842 60S RIBOSOMAL PROTEIN L31. [SWISSPROT;Acc:P12947] RPL31
1843 40S RIBOSOMAL PROTEIN S19. [SWISSPROT;Acc:P39019] RPS19
1844 0.917867 60S RIBOSOMAL PROTEIN L18A. [SWISSPROT;Acc:Q02543] 0.214359 no value 0.233540371
1845 0.107989 MITOCHONDRIAL RIBOSOMAL PROTEIN L22. [RefSeq;Acc:NM_014180] 0.0252117 MRPL22 0.233465446
1846 0.323185 MCT-1 PROTEIN. [RefSeq;Acc:NM_014060] 0.0754524 MCTS1 0.233465043
1847 0.924279 "SERYL-TRNA SYNTHETASE, MITOCHONDRIAL PRECURSOR (EC 6.1.1.11) (SERINE--TRNA LIGASE) (SERRSMT). [SWISSPROT;Acc:Q9NP81]" 0.215775 SARS2 0.233452237
1848 1.25677 SERYL-TRNA SYNTHETASE (EC 6.1.1.11) (SERINE--TRNA LIGASE) (SERRS). [SWISSPROT;Acc:P49591] 0.293395 SARS 0.233451626
1849 0.0962388 BA304I5.1 (NOVEL LIPASE) (FRAGMENT). [SPTREMBL;Acc:Q96LG2] 0.0224671 LIPM 0.233451581
1850 0.118126 "TRIACYLGLYCEROL LIPASE, GASTRIC PRECURSOR (EC 3.1.1.3) (GASTRIC LIPASE) (GL). [SWISSPROT;Acc:P07098]" 0.0275767 LIPF 0.233451569
1851 LYSOSOMAL ACID LIPASE/CHOLESTERYL ESTER HYDROLASE PRECURSOR (EC 3.1.1.13) (LAL) (ACID CHOLESTERYL ESTER HYDROLASE) (STEROL ESTERASE) (LIPASE A) (CHOLESTERYL ESTERASE). [SWISSPROT;Acc:P38571] LIPA

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/