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 Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1725 to 1774 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    Value Type
    description
    red
    green
    network_comparison
    432 Measured mitochondrial processing peptidase beta subunit, mitochondrial precursor (ec 3.4.24.64) (beta-mpp) (p-52). [swissprot;acc:o75439] 5244.71 6036.27 1.15093
    Ranked endonuclease g, mitochondrial precursor (ec 3.1.30.-) (endo g). [swissprot;acc:q14249] 212.547 229.411 1.07934
    Squared calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632] 29095.3 35337.6 1.21455
    Rooted leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71] 54.4927 49.6125 1.09837
    433 Measured mitochondrial processing peptidase alpha subunit, mitochondrial precursor (ec 3.4.24.64) (alpha-mpp) (p-55) (ha1523). [swissprot;acc:q10713] 5244.88 6036.38 1.15091
    Ranked programmed cell death protein 8, mitochondrial precursor (ec 1.-.-.-) (apoptosis-inducing factor). [swissprot;acc:o95831] 212.547 229.411 1.07934
    Squared grancalcin. [swissprot;acc:p28676] 29095.7 35338.3 1.21455
    Rooted laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047] 54.4927 49.6125 1.09837
    434 Measured ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930] 5246.38 6037.37 1.15077
    Ranked t-box transcription factor tbx6 (t-box protein 6). [swissprot;acc:o95947] 212.547 229.411 1.07934
    Squared splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] 18306.1 22230.6 1.21438
    Rooted thymic stromal co-transporter. [refseq;acc:nm_033051] 54.4927 49.6125 1.09837
    435 Measured proline synthetase co-transcribed bacterial homolog protein. [swissprot;acc:o94903] 5233.86 6022.6 1.1507
    Ranked polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] 221.522 205.286 1.07909
    Squared cytochrome b5 reductase b5r.2. [refseq;acc:nm_016229] 26598.9 32283.5 1.21372
    Rooted 60s ribosomal protein l19. [swissprot;acc:p14118] 50.832 46.3081 1.09769
    436 Measured arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069] 6230.94 7168.2 1.15042
    Ranked paxillin. [swissprot;acc:p49023] 221.522 205.286 1.07909
    Squared cytochrome b5 reductase 1 (b5r.1). [refseq;acc:nm_016243] 26598.9 32283.5 1.21372
    Rooted putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] 210.928 192.165 1.09764
    437 Measured suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55] 3779.92 4348.48 1.15042
    Ranked cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [swissprot;acc:q15642] 209.921 226.459 1.07878
    Squared nadh-cytochrome b5 reductase (ec 1.6.2.2) (b5r). [swissprot;acc:p00387] 26598.9 32283.5 1.21372
    Rooted zinc finger protein t86. [swissprot;acc:o00488] 51.0466 56.024 1.09751
    438 Measured swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [swissprot;acc:o14497] 6252.58 7192.88 1.15039
    Ranked n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227] 233.723 216.674 1.07869
    Squared arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069] 28863.2 35031.5 1.21371
    Rooted bag-family molecular chaperone regulator-3 (bcl-2 binding athanogene- 3) (bag-3) (bcl-2-binding protein bis) (docking protein cair-1). [swissprot;acc:o95817] 55.1867 60.5522 1.09722
    439 Measured programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340] 6252.58 7192.88 1.15039
    Ranked 40s ribosomal protein s9. [swissprot;acc:p46781] 238.986 257.784 1.07866
    Squared cell division cycle protein 23; anaphase-promoting complex subunit 8. [refseq;acc:nm_004661] 51616.7 42588.9 1.21198
    Rooted dok-like protein. [refseq;acc:nm_024872] 63.2134 69.352 1.09711
    440 Measured calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632] 6251.91 7192.08 1.15038
    Ranked highly expressed in cancer, rich in leucine heptad repeats. [refseq;acc:nm_006101] 231.802 249.983 1.07843
    Squared dna topoisomerase ii, alpha isozyme (ec 5.99.1.3). [swissprot;acc:p11388] 26348.4 31925.8 1.21168
    Rooted docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496] 63.2134 69.352 1.09711
    441 Measured grancalcin. [swissprot;acc:p28676] 6251.96 7192.13 1.15038
    Ranked grb2-related adaptor protein. [swissprot;acc:q13588] 223.457 207.222 1.07835
    Squared dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880] 26348.7 31924.3 1.21161
    Rooted docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704] 63.2134 69.352 1.09711
    442 Measured sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] 6251.99 7192.17 1.15038
    Ranked e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140] 223.802 207.55 1.0783
    Squared centromere protein j; centrosomal p4.1-associated protein; lyst-interacting protein lip1; lag-3-associated protein. [refseq;acc:nm_018451] 51286.6 42334.5 1.21146
    Rooted tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685] 63.2134 69.352 1.09711
    443 Measured brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732] 6252.27 7192.51 1.15038
    Ranked neuron navigator 2 isoform l; retinoic acid inducible in neuroblastoma; pore membrane and/or filament interacting like protein 2; helicase helad1. [refseq;acc:nm_145117] 223.79 207.539 1.0783
    Squared translation initiation factor if-2, mitochondrial precursor (if-2mt) (if-2(mt)). [swissprot;acc:p46199] 26472.8 32067.7 1.21135
    Rooted 60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025] 50.1766 45.7369 1.09707
    444 Measured probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848] 3758.67 4322.87 1.15011
    Ranked neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443] 223.801 207.549 1.0783

    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
    - 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/