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 Value Type Network Comparison Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 63924 to 63973 of 66312 in total
    Interaction Map  : Low confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		Network Comparison Type
    		red
    		network_comparison
    		green
    4763 RAB23 ras-related protein rab-23 (hspc137). [swissprot;acc:q9ulc3] Measured Divided 8550.04 1.01278 8659.33
    SMS spermine synthase (ec 2.5.1.22) (spermidine aminopropyltransferase) (spmsy). [swissprot;acc:p52788] Ranked Subtracted 201.116 1.009 200.107
    STXBP1 syntaxin binding protein 1 (unc-18 homolog) (unc-18a) (unc-18-1) (n- sec1) (rbsec1) (p67). [swissprot;acc:q64320] Divided 200.018 1.00493 199.036
    TRIP10 cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [swissprot;acc:q15642] Squared 44782.1 1.01241 44233
    Subtracted 549.1
    4764 ANAPC1 anaphase-promoting complex 1 (meiotic checkpoint regulator). [refseq;acc:nm_022662] Ranked Divided 200.161 1.00492 201.146
    APOA1BP apolipoprotein a-i binding protein; apoa-i binding protein. [refseq;acc:nm_144772] Squared 47975.2 1.01238 47388.3
    CDK8 cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336] Rooted Subtracted 70.3213 1.1791 71.5004
    CTBP2 c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545] Measured 10232.6 102.4 10130.2
    ELOVL4 elongation of very long chain fatty acids protein 4. [swissprot;acc:q9gzr5] Rooted Divided 70.3734 1.01676 71.5529
    FZR1 fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263] Squared Subtracted 46042.5 541.5 46584
    ITGB1BP3 muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446] Ranked 196.724 1.003 197.727
    MRPS33 mitochondrial 28s ribosomal protein s33 (s33mt) (mrp-s33) (cgi-139) (ptd003). [swissprot;acc:q9y291] Measured Divided 8550.04 1.01278 8659.33
    4765 no value 60s ribosomal protein l9. [swissprot;acc:p32969] Subtracted 7416.2 102.17 7518.37
    ANAPC1 anaphase-promoting complex 1 (meiotic checkpoint regulator). [refseq;acc:nm_022662] Ranked 200.161 0.985 201.146
    CDC2L6 cyclin-dependent kinase (cdc2-like) 11; death-preventing kinase. [refseq;acc:nm_015076] Rooted 70.3218 1.1784 71.5002
    LYST lysosomal trafficking regulator (beige homolog). [swissprot;acc:q99698] Measured Divided 8232.92 1.01275 8337.89
    MLH1 dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692] Squared Subtracted 47993.1 539.7 47453.4
    PDPK1 3-phosphoinositide dependent protein kinase-1 (ec 2.7.1.37) (hpdk1). [swissprot;acc:o15530] Ranked Divided 206.842 1.00492 205.83
    PICK1 prkca-binding protein (protein kinase c-alpha binding protein) (protein interacting with c kinase 1). [swissprot;acc:q9nrd5] Rooted 71.8821 1.01668 73.0812
    RGS19 regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795] Squared 41196.2 1.01235 40693.7
    4766 no value gamma-interferon inducible lysosomal thiol reductase precursor (gamma-interferon-inducible protein ip-30). [swissprot;acc:p13284] Measured 8232.92 1.01275 8337.89
    ATP6AP2 vacuolar atp synthase membrane sector associated protein m8-9 (v-atpase m8.9 subunit). [swissprot;acc:o75787] Squared Subtracted 50149.6 538.8 49610.8
    IPO13 importin 13; ran binding protein 13. [refseq;acc:nm_014652] Measured 8127.17 101.68 8228.85
    PCMT1 protein-l-isoaspartate(d-aspartate) o-methyltransferase (ec 2.1.1.77) (protein-beta-aspartate methyltransferase) (pimt) (protein l- isoaspartyl/d-aspartyl methyltransferase) (l-isoaspartyl protein carboxyl methyltransferase). [swissprot;acc:p22061] Ranked Divided 206.842 1.00492 205.83
    PHC3 polyhomeotic like 3; early development regulator 3; polyhomeotic 3. [refseq;acc:nm_024947] Rooted 73.0124 1.01661 74.2254
    RGS20 regulator of g-protein signaling 20 (rgs20) (regulator of gz- selective protein signaling 1) (gz-selective gtpase-activating protein) (g(z)gap). [swissprot;acc:o76081] Squared 41196.2 1.01235 40693.7
    SAMSN1 sam-domain protein samsn-1 (sam domain, sh3 domain and nuclear localisation signals protein 1). [swissprot;acc:q9nsi8] Rooted Subtracted 72.6624 1.1749 71.4875
    STXBP1 syntaxin binding protein 1 (unc-18 homolog) (unc-18a) (unc-18-1) (n- sec1) (rbsec1) (p67). [swissprot;acc:q64320] Ranked 200.018 0.982 199.036
    4767 CHEK1 serine/threonine-protein kinase chk1 (ec 2.7.1.-). [swissprot;acc:o14757] Squared 50149.6 538.8 49610.8
    CTRL proteasome subunit beta type 10 precursor (ec 3.4.25.1) (proteasome mecl-1) (macropain subunit mecl-1) (multicatalytic endopeptidase complex subunit mecl-1). [swissprot;acc:p40306] Measured 7877.1 100.68 7977.78
    MLL5 myeloid/lymphoid or mixed-lineage leukemia 5 (trithorax homolog, drosophila). [refseq;acc:nm_182931] Divided 7836.97 1.01267 7936.3
    PIGS gpi transamidase component pig-s (phosphatidylinositol-glycan biosynthesis, class s protein). [swissprot;acc:q96s52] Ranked 198.971 1.00491 197.998
    Subtracted 0.973
    RGS17 regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6] Squared Divided 41196.2 1.01235 40693.7
    RPL19 60s ribosomal protein l19. [swissprot;acc:p14118] Rooted 69.3079 1.01656 70.4555
    SASH1 sam and sh3 domain containing 1. [refseq;acc:nm_015278] Subtracted 72.6632 1.1737 71.4895
    4768 BOK bcl2-related ovarian killer. [refseq;acc:nm_032515] Squared 27306.3 537.8 26768.5
    CSRP3 lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461] Rooted Divided 69.2825 1.01648 70.4241
    GNAO1 guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471] Squared 41196.2 1.01235 40693.7
    MRPL3 mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001] Rooted Subtracted 69.2175 1.1735 70.391
    PITRM1 metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] Ranked Divided 188.213 1.0049 187.295
    STX10 syntaxin 10 (syn10). [swissprot;acc:o60499] Subtracted 203.126 0.971 202.155
    VPS4A vacuolar protein sorting factor 4a; skd1-homolog; vacuolar sorting protein 4. [refseq;acc:nm_013245] Measured 7772.88 100.6 7873.48
    YLPM1 nuclear protein zap3 (zap113). [swissprot;acc:p49750] Divided 8167.12 1.0126 8270.02
    4769 ATG3 apg3p; pc3-96 protein. [refseq;acc:nm_022488] Ranked 177.446 1.00481 176.597
    EXOSC5 exosome complex exonuclease rrp46 (ec 3.1.13.-) (ribosomal rna processing protein 46) (p12b) (chronic myelogenous leukemia tumor antigen 28). [swissprot;acc:q9nqt4] Subtracted 202.127 0.934 201.193
    GYS2 glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840] Measured Divided 8857 1.01253 8967.97
    PRAM1 pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152] Rooted Subtracted 71.2585 1.1712 72.4297
    SAMSN1 sam-domain protein samsn-1 (sam domain, sh3 domain and nuclear localisation signals protein 1). [swissprot;acc:q9nsi8] Divided 72.6624 1.01644 71.4875

    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/