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:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene description measured expected final Hugo
Results: HTML CSV LaTeX Showing element 1808 to 1857 of 3206 in total
Rank
description
measured
expected
final
Hugo
1808 0.146293 0.623804 0.234517573 MED9
1809 CARBOXYPEPTIDASE A5. [RefSeq;Acc:NM_080385] 0.0167711 0.0715398 0.234430345 CPA5
1810 CARBOXYPEPTIDASE A1 PRECURSOR (EC 3.4.17.1). [SWISSPROT;Acc:P15085] 0.0213901 0.0912429 0.234430295 CPA1
1811 AMINOACYLASE-1 (EC 3.5.1.14) (N-ACYL-L-AMINO-ACID AMIDOHYDROLASE) (ACY-1). [SWISSPROT;Acc:Q03154] 0.18122 0.773023 0.234430282 ACY1
1812 "NEUTRAL AND BASIC AMINO ACID TRANSPORT PROTEIN RBAT (B(0,+)-TYPE AMINO ACID TRANSPORT PROTEIN) (NBAT) (D2H). [SWISSPROT;Acc:Q07837]" 0.0214423 0.0914656 0.234430212 SLC3A1
1813 CARBOXYPEPTIDASE B PRECURSOR (EC 3.4.17.2) (PANCREAS-SPECIFIC PROTEIN) (PASP). [SWISSPROT;Acc:P15086] 0.0139875 0.059666 0.234429994 CPB1
1814 60S RIBOSOMAL PROTEIN L9. [SWISSPROT;Acc:P32969] 0.788679 3.36493 0.234381993 no value
1815 PROTEASOME SUBUNIT ALPHA TYPE 7-LIKE (EC 3.4.25.1). [SWISSPROT;Acc:Q8TAA3] 0.726532 3.09996 0.234368185 PSMA8
1816 UNC-119 PROTEIN HOMOLOG (RETINAL PROTEIN 4) (HRG4). [SWISSPROT;Acc:Q13432] 0.183433 0.783008 0.234267083 UNC119
1817 DNA FRAGMENTATION FACTOR ALPHA SUBUNIT (DNA FRAGMENTATION FACTOR 45 KDA SUBUNIT) (DFF-45) (INHIBITOR OF CAD) (ICAD). [SWISSPROT;Acc:O00273] 0.0764303 0.326253 0.234266965 DFFA
1818 ANKYRIN 3 (ANK-3) (ANKYRIN G). [SWISSPROT;Acc:Q12955] 0.0299967 0.128045 0.234266859 ANK3
1819 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 0.326867 0.234266842 ADAMTS9
1820 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 8 (26S PROTEASOME REGULATORY SUBUNIT S14) (P31). [SWISSPROT;Acc:P48556] 0.824134 3.51793 0.234266742 PSMD8
1821 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 0.654349 0.234266424 DFFB
1822 ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 3. [SWISSPROT;Acc:P36405] 0.038359 0.163741 0.234266311 ARL3
1823 no value
1824 "ANKYRIN 2 (BRAIN ANKYRIN) (ANKYRIN B) (ANKYRIN, NONERYTHROID). [SWISSPROT;Acc:Q01484]" ANK2
1825 0.341137 1.45621 0.234263602 RFK
1826 PROTEASOME SUBUNIT ALPHA TYPE 7 (EC 3.4.25.1) (PROTEASOME SUBUNIT RC6-1) (PROTEASOME SUBUNIT XAPC7). [SWISSPROT;Acc:O14818] 0.813157 3.47138 0.234246035 PSMA7
1827 "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 2.20733 0.234222794 PPP2CA
1828 S-ADENOSYLMETHIONINE SYNTHETASE ALPHA AND BETA FORMS (EC 2.5.1.6) (METHIONINE ADENOSYLTRANSFERASE) (ADOMET SYNTHETASE) (MAT-I/III). [SWISSPROT;Acc:Q00266] 0.53545 2.28647 0.234181949 MAT1A
1829 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 0.0954818 0.234085449 CASP3
1830 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 0.120482 0.23408476 CASP7
1831 0.263169 1.12425 0.234084056 TSR1
1832 VALYL-TRNA SYNTHETASE 2 (EC 6.1.1.9) (VALINE--TRNA LIGASE 2) (VALRS 2) (G7A). [SWISSPROT;Acc:P26640] 0.0546688 0.233559 0.234068479 VARS
1833 N-ACETYLTRANSFERASE 5 (EC 2.3.1.-). [SWISSPROT;Acc:Q9Y6D2] 0.101148 0.43244 0.233900657 NAT5
1834 RIBOSOMAL PROTEIN L24-LIKE; 60S RIBOSOMAL PROTEIN L30 ISOLOG; MY024 PROTEIN; HOMOLOG OF YEAST RIBOSOMAL LIKE PROTEIN 24. [RefSeq;Acc:NM_016304] 0.193647 0.827963 0.23388364 C15orf15
1835 DNA-DIRECTED RNA POLYMERASE II 7.6 KDA POLYPEPTIDE (EC 2.7.7.6) (RPB10) (RPB7.6) (RPABC5). [SWISSPROT;Acc:P52436] 0.508074 2.17246 0.233870359 POLR2L
1836 U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM1 (SMALL NUCLEAR RIBONUCLEAR CASM) (CANCER-ASSOCIATED SM-LIKE). [SWISSPROT;Acc:O15116] 0.31086 1.32969 0.233783814 LSM1
1837 0.0766245 0.327833 0.233730283 C8orf53
1838 0.0910964 0.38998 0.233592492 MTHFD1L
1839 40S RIBOSOMAL PROTEIN S24 (S19). [SWISSPROT;Acc:P16632] 0.182207 0.780167 0.233548715 RPS24
1840 0.0267948 0.114733 0.233540481 C18orf22
1841 60S RIBOSOMAL PROTEIN L39. [SWISSPROT;Acc:P02404] 0.187564 0.803133 0.233540397 no value
1842 60S RIBOSOMAL PROTEIN L31. [SWISSPROT;Acc:P12947] RPL31
1843 40S RIBOSOMAL PROTEIN S19. [SWISSPROT;Acc:P39019] RPS19
1844 60S RIBOSOMAL PROTEIN L18A. [SWISSPROT;Acc:Q02543] 0.214359 0.917867 0.233540371 no value
1845 MITOCHONDRIAL RIBOSOMAL PROTEIN L22. [RefSeq;Acc:NM_014180] 0.0252117 0.107989 0.233465446 MRPL22
1846 MCT-1 PROTEIN. [RefSeq;Acc:NM_014060] 0.0754524 0.323185 0.233465043 MCTS1
1847 "SERYL-TRNA SYNTHETASE, MITOCHONDRIAL PRECURSOR (EC 6.1.1.11) (SERINE--TRNA LIGASE) (SERRSMT). [SWISSPROT;Acc:Q9NP81]" 0.215775 0.924279 0.233452237 SARS2
1848 SERYL-TRNA SYNTHETASE (EC 6.1.1.11) (SERINE--TRNA LIGASE) (SERRS). [SWISSPROT;Acc:P49591] 0.293395 1.25677 0.233451626 SARS
1849 BA304I5.1 (NOVEL LIPASE) (FRAGMENT). [SPTREMBL;Acc:Q96LG2] 0.0224671 0.0962388 0.233451581 LIPM
1850 "TRIACYLGLYCEROL LIPASE, GASTRIC PRECURSOR (EC 3.1.1.3) (GASTRIC LIPASE) (GL). [SWISSPROT;Acc:P07098]" 0.0275767 0.118126 0.233451569 LIPF
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
1852 PRESENILIN-LIKE PROTEIN 1 (EC 3.4.99.-) (SPPL2B PROTEIN). [SWISSPROT;Acc:Q8TCT7] 0.0331615 0.142049 0.233451133 no value
1853
1854 0.0274494 0.117581 0.233450983
1855 PRESENILIN-LIKE PROTEIN 2 (EC 3.4.99.-) (SPPL2A PROTEIN). [SWISSPROT;Acc:Q8TCT8] 0.0275157 0.117865 0.233450982
1856 GTP-BINDING NUCLEAR PROTEIN RAN (TC4) (RAN GTPASE) (ANDROGEN RECEPTOR- ASSOCIATED PROTEIN 24). [SWISSPROT;Acc:P17080] 0.46892 2.00865 0.233450327 RANP1
1857 0.0252313 0.108089 0.233430784 FCF1

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/