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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

  • value_type as 'ranked' since this provides a very robust analysis method.
  • intercation map as 'high confidence'
  • network_comparison type as 'Divided' since this leads to a natural grouping of similar proteins
  • filtered as 'true' since this will only use the microarray measurements that have a sufficiently large confidence level.

    • 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 Hugo description Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1758 to 1807 of 6456 in total
    Value Type  : Ranked
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Network Comparison Type
    		red
    		green
    		network_comparison
    879 PRKAB1 5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478] Divided 212.002 203.954 1.03946
    880 FARS2 phenylalanine-trna synthetase. [refseq;acc:nm_006567] Subtracted 217.491 209.323 8.168
    PRKAG2 5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0] Divided 212.002 203.954 1.03946
    881 BTF3 transcription factor btf3 (rna polymerase b transcription factor 3). [swissprot;acc:p20290] Subtracted 211.961 203.814 8.147
    MYCL1 l-myc-1 proto-oncogene protein. [swissprot;acc:p12524] Divided 227.604 219.001 1.03928
    882 MYCN n-myc proto-oncogene protein. [swissprot;acc:p04198] 227.601 219.008 1.03924
    TOMM20 mitochondrial import receptor subunit tom20 homolog (mitochondrial 20 kda outer membrane protein) (outer mitochondrial membrane receptor tom20). [swissprot;acc:q15388] Subtracted 198.781 190.66 8.121
    883 GABPA ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [swissprot;acc:q06546] Divided 227.596 219.017 1.03917
    PEX19 peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [swissprot;acc:p40855] Subtracted 198.781 190.66 8.121
    884 no value ga binding protein beta-2 chain (gabp-beta-2 subunit) (transcription factor e4tf1-47) (gapbp-2) (nuclear respiratory factor-2 subunit gamma). [swissprot;acc:q06545] Divided 227.596 219.017 1.03917
    sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [refseq;acc:nm_016538] Subtracted 232.473 224.372 8.101
    885 casein kinase ii beta chain (ck ii) (phosvitin) (g5a). [swissprot;acc:p13862]
    NDUFS8 nadh-ubiquinone oxidoreductase 23 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-23kd) (ci-23kd) (tyky subunit). [swissprot;acc:o00217] Divided 227.596 219.017 1.03917
    886 no value transcription factor btf3 homolog 3. [swissprot;acc:q13892] Subtracted 211.908 203.832 8.076
    ELOVL1 elongation of very long chain fatty acids protein 1 (cgi-88). [swissprot;acc:q9bw60] Divided 227.596 219.018 1.03917
    887 PRKAG1 5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619] Subtracted 212.002 203.954 8.048
    TBL3 transducin beta-like 3; wd-repeat protein sazd. [refseq;acc:nm_006453] Divided 244.155 234.96 1.03913
    888 no value nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594] 212.027 204.05 1.03909
    PRKAA2 5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646] Subtracted 212.002 203.954 8.048
    889 no value alpha-nac protein. [sptrembl;acc:q9h009] Divided 212.028 204.053 1.03908
    PRKAA1 5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131] Subtracted 212.002 203.954 8.048
    890 PRKAB2 5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741]
    STX7 syntaxin 7. [swissprot;acc:o15400] Divided 217.181 209.012 1.03908
    891 DIRAS1 small gtp-binding tumor suppressor 1. [refseq;acc:nm_145173] 212.028 204.055 1.03907
    PRKAG3 5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9] Subtracted 212.002 203.954 8.048
    892 DIRAS2 di-ras2. [refseq;acc:nm_017594] Divided 212.028 204.055 1.03907
    PRKAB1 5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478] Subtracted 212.002 203.954 8.048
    893 MYC myc proto-oncogene protein (c-myc). [swissprot;acc:p01106] Divided 227.585 219.037 1.03903
    PRKAG2 5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0] Subtracted 212.002 203.954 8.048
    894 FARSA phenylalanyl-trna synthetase alpha chain (ec 6.1.1.20) (phenylalanine- -trna ligase alpha chain) (phers) (cml33). [swissprot;acc:q9y285] Divided 217.491 209.323 1.03902
    MRPL27 mitochondrial 60s ribosomal protein l27 (l27mt) (hspc250). [swissprot;acc:q9p0m9] Subtracted 231.163 239.205 8.042
    895 ACADVL acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] 164 155.961 8.039
    FARS2 phenylalanine-trna synthetase. [refseq;acc:nm_006567] Divided 217.491 209.323 1.03902
    896 POLR2J dna-directed rna polymerase ii 13.3 kda polypeptide (ec 2.7.7.6) (rpb11). [swissprot;acc:p52435] 230.811 239.785 1.03888
    WDR36 t-cell activation wd repeat protein. [refseq;acc:nm_139281] Subtracted 243.34 235.322 8.018
    897 PDPK1 3-phosphoinositide dependent protein kinase-1 (ec 2.7.1.37) (hpdk1). [swissprot;acc:o15530] Divided 272.878 283.472 1.03882
    TGS1 prip-interacting protein pipmt; prip-interacting protein with methyltransferase domain. [refseq;acc:nm_024831] Subtracted 210.863 218.878 8.015
    898 no value 60s acidic ribosomal protein p1. [swissprot;acc:p05386] Divided 229.171 238.048 1.03874
    GOPC pdz/coiled-coil domain binding partner for the rho-family gtpase tc10; fused in glioblastoma; golgi associated pdz and coiled-coil motif containing protein; cftr-associated ligand. [refseq;acc:nm_020399] Subtracted 210.863 218.878 8.015
    899 no value nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594] 212.027 204.05 7.977
    TXNDC2 thioredoxin domain-containing 2; sperm-specific thioredoxin; thioredoxin domain-containing 2 (spermatozoa). [refseq;acc:nm_032243] Divided 229.171 238.048 1.03874
    900 no value alpha-nac protein. [sptrembl;acc:q9h009] Subtracted 212.028 204.053 7.975
    TXN thioredoxin (atl-derived factor) (adf) (surface associated sulphydryl protein) (sasp). [swissprot;acc:p10599] Divided 229.171 238.048 1.03874
    901 DIRAS1 small gtp-binding tumor suppressor 1. [refseq;acc:nm_145173] Subtracted 212.028 204.055 7.973
    SSRP1 structure-specific recognition protein 1 (ssrp1) (recombination signal sequence recognition protein) (t160) (chromatin-specific transcription elongation factor 80 kda subunit) (fact 80 kda subunit). [swissprot;acc:q08945] Divided 237.62 228.762 1.03872
    902 DIRAS2 di-ras2. [refseq;acc:nm_017594] Subtracted 212.028 204.055 7.973
    SUPT16H chromatin-specific transcription elongation factor large subunit. [refseq;acc:nm_007192] Divided 237.62 228.762 1.03872
    903 no value uba/ubx 33.3 kda protein. [swissprot;acc:q04323] Subtracted 217.168 209.207 7.961
    EIF3G eukaryotic translation initiation factor 3 subunit 4 (eif-3 delta) (eif3 p44) (eif-3 rna-binding subunit) (eif3 p42) (eif3g). [swissprot;acc:o75821] Divided 246.354 237.223 1.03849
    904 CIRH1A cirhin; testis expressed gene 292; cirrhosis, autosomal recessive 1a. [refseq;acc:nm_032830] Subtracted 243.312 235.351 7.961

    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 HGNC identifier if it exists
    - Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
    - Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
    - Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
    - Filtered specifies whether we only included the high confidence microarry measurements or not.
    - http://analysis.yellowcouch.org/