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 Value Type 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
    		description
    		Hugo
    		Value Type
    		red
    		green
    		network_comparison
    432 calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632] CAPNS1 Squared 29095.3 35337.6 1.21455
    endonuclease g, mitochondrial precursor (ec 3.1.30.-) (endo g). [swissprot;acc:q14249] ENDOG Ranked 212.547 229.411 1.07934
    leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71] LRRC3 Rooted 54.4927 49.6125 1.09837
    mitochondrial processing peptidase beta subunit, mitochondrial precursor (ec 3.4.24.64) (beta-mpp) (p-52). [swissprot;acc:o75439] PMPCB Measured 5244.71 6036.27 1.15093
    433 grancalcin. [swissprot;acc:p28676] GCA Squared 29095.7 35338.3 1.21455
    laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047] LAMC1 Rooted 54.4927 49.6125 1.09837
    mitochondrial processing peptidase alpha subunit, mitochondrial precursor (ec 3.4.24.64) (alpha-mpp) (p-55) (ha1523). [swissprot;acc:q10713] PMPCA Measured 5244.88 6036.38 1.15091
    programmed cell death protein 8, mitochondrial precursor (ec 1.-.-.-) (apoptosis-inducing factor). [swissprot;acc:o95831] AIFM1 Ranked 212.547 229.411 1.07934
    434 splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] SF3B1 Squared 18306.1 22230.6 1.21438
    t-box transcription factor tbx6 (t-box protein 6). [swissprot;acc:o95947] TBX6 Ranked 212.547 229.411 1.07934
    thymic stromal co-transporter. [refseq;acc:nm_033051] SLC46A2 Rooted 54.4927 49.6125 1.09837
    ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930] UQCRC1 Measured 5246.38 6037.37 1.15077
    435 60s ribosomal protein l19. [swissprot;acc:p14118] RPL19 Rooted 50.832 46.3081 1.09769
    cytochrome b5 reductase b5r.2. [refseq;acc:nm_016229] CYB5R2 Squared 26598.9 32283.5 1.21372
    polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] POLI Ranked 221.522 205.286 1.07909
    proline synthetase co-transcribed bacterial homolog protein. [swissprot;acc:o94903] PROSC Measured 5233.86 6022.6 1.1507
    436 arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069] SORBS2 6230.94 7168.2 1.15042
    cytochrome b5 reductase 1 (b5r.1). [refseq;acc:nm_016243] CYB5R1 Squared 26598.9 32283.5 1.21372
    paxillin. [swissprot;acc:p49023] PXN Ranked 221.522 205.286 1.07909
    putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] UBAC1 Rooted 210.928 192.165 1.09764
    437 cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [swissprot;acc:q15642] TRIP10 Ranked 209.921 226.459 1.07878
    nadh-cytochrome b5 reductase (ec 1.6.2.2) (b5r). [swissprot;acc:p00387] CYB5R3 Squared 26598.9 32283.5 1.21372
    suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55] PPAN-P2RY11 Measured 3779.92 4348.48 1.15042
    zinc finger protein t86. [swissprot;acc:o00488] ZNF593 Rooted 51.0466 56.024 1.09751
    438 arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069] SORBS2 Squared 28863.2 35031.5 1.21371
    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] BAG3 Rooted 55.1867 60.5522 1.09722
    n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227] ARD1A Ranked 233.723 216.674 1.07869
    swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [swissprot;acc:o14497] ARID1A Measured 6252.58 7192.88 1.15039
    439 40s ribosomal protein s9. [swissprot;acc:p46781] RPS9 Ranked 238.986 257.784 1.07866
    cell division cycle protein 23; anaphase-promoting complex subunit 8. [refseq;acc:nm_004661] CDC23 Squared 51616.7 42588.9 1.21198
    dok-like protein. [refseq;acc:nm_024872] no value Rooted 63.2134 69.352 1.09711
    programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340] PDCD6 Measured 6252.58 7192.88 1.15039
    440 calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632] CAPNS1 6251.91 7192.08 1.15038
    dna topoisomerase ii, alpha isozyme (ec 5.99.1.3). [swissprot;acc:p11388] no value Squared 26348.4 31925.8 1.21168
    docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496] DOK2 Rooted 63.2134 69.352 1.09711
    highly expressed in cancer, rich in leucine heptad repeats. [refseq;acc:nm_006101] NDC80 Ranked 231.802 249.983 1.07843
    441 dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880] TOP2B Squared 26348.7 31924.3 1.21161
    docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704] DOK1 Rooted 63.2134 69.352 1.09711
    grancalcin. [swissprot;acc:p28676] GCA Measured 6251.96 7192.13 1.15038
    grb2-related adaptor protein. [swissprot;acc:q13588] GRAP Ranked 223.457 207.222 1.07835
    442 centromere protein j; centrosomal p4.1-associated protein; lyst-interacting protein lip1; lag-3-associated protein. [refseq;acc:nm_018451] CENPJ Squared 51286.6 42334.5 1.21146
    e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140] ANKS1B Ranked 223.802 207.55 1.0783
    sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] SRI Measured 6251.99 7192.17 1.15038
    tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685] FRK Rooted 63.2134 69.352 1.09711
    443 60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025] no value 50.1766 45.7369 1.09707
    brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732] ARID1B Measured 6252.27 7192.51 1.15038
    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] NAV2 Ranked 223.79 207.539 1.0783
    translation initiation factor if-2, mitochondrial precursor (if-2mt) (if-2(mt)). [swissprot;acc:p46199] MTIF2 Squared 26472.8 32067.7 1.21135
    444 60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] no value Rooted 50.1636 45.7275 1.09701
    neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443] NAV1 Ranked 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
    - 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/