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 description Hugo Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 841 to 890 of 3228 in total
    Network Comparison Type  : Divided
    Value Type  : Ranked
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		red
    		green
    		network_comparison
    841 peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [swissprot;acc:p40855] PEX19 198.781 190.66 1.04259
    842 jm1 protein. [refseq;acc:nm_014008] CCDC22 219.762 210.806 1.04248
    843 trifunctional purine biosynthetic protein adenosine-3 [includes: phosphoribosylamine--glycine ligase (ec 6.3.4.13) (gars) (glycinamide ribonucleotide synthetase) (phosphoribosylglycinamide synthetase); phosphoribosylformylglycinamidine cyclo-ligase (ec 6.3.3.1) (airs) (phosphoribosyl-aminoimidazole synthetase) (air synthase); phosphoribosylglycinamide formyltransferase (ec 2.1.2.2) (gart) (gar transformylase) (5'-phosphoribosylglycinamide transformylase)]. [swissprot;acc:p22102] GART 218.521 227.796 1.04244
    844 c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596] CLEC3A 178.033 170.82 1.04223
    845 u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [swissprot;acc:o15116] LSM1 228.599 219.399 1.04193
    846 methyltransferase like 2. [refseq;acc:nm_018396] no value 147.211 153.371 1.04184
    847 cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763] DYNLT1
    848 fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263] FZR1
    849 proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [swissprot;acc:q92824] PCSK5
    850 cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693] CPSF4 107.842 112.329 1.04161
    851 trs85 homolog. [swissprot;acc:q9y2l5] KIAA1012
    852 hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492] HPRT1 193.114 185.412 1.04154
    853 wd-repeat protein wdc146. [swissprot;acc:q9c0j8] WDR33 108.289 112.772 1.0414
    854 cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] CPSF1
    855 tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452] CLEC3B 178.514 171.42 1.04138
    856 xenotropic and polytropic retrovirus receptor. [refseq;acc:nm_004736] XPR1 215.028 206.623 1.04068
    857 putatative 28 kda protein. [refseq;acc:nm_020143] PNO1 227.241 236.467 1.0406
    858 syntaxin 12. [refseq;acc:nm_177424] STX12 217.446 208.997 1.04043
    859 60s ribosomal protein l39. [swissprot;acc:p02404] no value 234.025 224.958 1.04031
    860 60s ribosomal protein l18a. [swissprot;acc:q02543]
    861 40s ribosomal protein s19. [swissprot;acc:p39019] RPS19
    862 60s ribosomal protein l31. [swissprot;acc:p12947] RPL31
    863 casein kinase ii, alpha chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19138] CSNK2A1P 240.194 230.957 1.03999
    864 casein kinase ii, alpha' chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19784] CSNK2A2
    865 transcription factor btf3 (rna polymerase b transcription factor 3). [swissprot;acc:p20290] BTF3 211.961 203.814 1.03997
    866 signal recognition particle 68 kda protein (srp68). [swissprot;acc:q9uhb9] SRP68 221.306 212.806 1.03994
    867 40s ribosomal protein s3a. [swissprot;acc:p49241] no value 225.689 234.674 1.03981
    868 diphosphomevalonate decarboxylase (ec 4.1.1.33) (mevalonate pyrophosphate decarboxylase) (mevalonate (diphospho)decarboxylase). [swissprot;acc:p53602] MVD 233.298 242.571 1.03975
    869 exocyst complex component sec8. [swissprot;acc:q96a65] EXOC4 217.762 209.449 1.03969
    870 transcription factor btf3 homolog 3. [swissprot;acc:q13892] no value 211.908 203.832 1.03962
    871 cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] CPSF2 110.2 114.552 1.03949
    872 heterogeneous nuclear ribonucleoprotein k (hnrnp k) (dc-stretch binding protein) (csbp) (transformation upregulated nuclear protein) (tunp). [swissprot;acc:q07244] HNRPK 224.413 233.272 1.03948
    873 u4/u6 small nuclear ribonucleoprotein prp4 (u4/u6 snrnp 60 kda protein) (wd splicing factor prp4) (hprp4). [swissprot;acc:o43172] PRPF4
    874 5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619] PRKAG1 212.002 203.954 1.03946
    875 5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646] PRKAA2
    876 5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131] PRKAA1
    877 5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741] PRKAB2
    878 5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9] PRKAG3
    879 5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478] PRKAB1
    880 5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0] PRKAG2
    881 l-myc-1 proto-oncogene protein. [swissprot;acc:p12524] MYCL1 227.604 219.001 1.03928
    882 n-myc proto-oncogene protein. [swissprot;acc:p04198] MYCN 227.601 219.008 1.03924
    883 ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [swissprot;acc:q06546] GABPA 227.596 219.017 1.03917
    884 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] no value
    885 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] NDUFS8
    886 elongation of very long chain fatty acids protein 1 (cgi-88). [swissprot;acc:q9bw60] ELOVL1 219.018
    887 transducin beta-like 3; wd-repeat protein sazd. [refseq;acc:nm_006453] TBL3 244.155 234.96 1.03913
    888 nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594] no value 212.027 204.05 1.03909
    889 alpha-nac protein. [sptrembl;acc:q9h009] 212.028 204.053 1.03908
    890 syntaxin 7. [swissprot;acc:o15400] STX7 217.181 209.012

    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/