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 green network_comparison
    Results: HTML CSV LaTeX Showing element 3001 to 3050 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		red
    		green
    		network_comparison
    751 no value ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] Squared 20305.9 23689.4 1.16663
    u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695] Ranked 223.463 212.875 1.04974
    MYL3 myosin light chain 1, slow-twitch muscle b/ventricular isoform (mlc1sb) (alkali). [swissprot;acc:p08590] Measured 4565.34 5085.92 1.11403
    PRKAA2 5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646] Rooted 66.9738 71.4638 1.06704
    752 NDUFS6 nadh-ubiquinone oxidoreductase 13 kda-a subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-a) (ci-13kd-a). [swissprot;acc:o75380] Measured 4565.34 5085.92 1.11403
    PRKAA1 5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131] Rooted 66.9736 71.4636 1.06704
    SLU7 step ii splicing factor slu7. [refseq;acc:nm_006425] Ranked 223.463 212.875 1.04974
    SNRPA1 u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661] Squared 20305.9 23689.4 1.16663
    753 HLCS biotin--protein ligase (ec 6.3.4.-) (biotin apo-protein ligase) [includes: biotin--[methylmalonyl-coa-carboxyltransferase] ligase (ec 6.3.4.9); biotin--[propionyl-coa-carboxylase [atp-hydrolyzing]] ligase (ec 6.3.4.10) (holocarboxylase synthetase) (hcs); biotin--[methylcrotonoyl-coa-carboxylase] ligase (ec 6.3.4.11); biotin--[acetyl-coa-carboxylase] ligase (ec 6.3.4.15)]. [swissprot;acc:p50747] 24183.6 28211.1 1.16654
    LBP lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428] Ranked 224.434 235.583 1.04968
    MYL6 myosin light chain 1, slow-twitch muscle a isoform (mlc1sa) (alkali). [swissprot;acc:p14649] Measured 4565.34 5085.92 1.11403
    PRKAB2 5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741] Rooted 66.9737 71.4637 1.06704
    754 no value myosin light chain 1, embryonic muscle/atrial isoform (pro1957). [swissprot;acc:p12829] Measured 4565.34 5085.92 1.11403
    BCAT1 branched-chain amino acid aminotransferase, cytosolic (ec 2.6.1.42) (bcat(c)) (eca39 protein). [swissprot;acc:p54687] Squared 23958.6 27945.1 1.16639
    PRKAG3 5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9] Rooted 66.9737 71.4637 1.06704
    SPCS2 microsomal signal peptidase 25 kda subunit (ec 3.4.-.-) (spase 25 kda subunit) (spc25). [swissprot;acc:q15005] Ranked 224.434 235.583 1.04968
    755 BCAT2 branched-chain amino acid aminotransferase, mitochondrial precursor (ec 2.6.1.42) (bcat(m)) (placental protein 18) (pp18). [swissprot;acc:o15382] Squared 23966.4 27952.2 1.16631
    NOL6 nucleolar rna-associated protein alpha isoform. [refseq;acc:nm_022917] Measured 4079.81 4545.01 1.11402
    PRKAB1 5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478] Rooted 66.9737 71.4637 1.06704
    UMPS uridine 5'-monophosphate synthase (ump synthase) [includes: orotate phosphoribosyltransferase (ec 2.4.2.10) (oprtase); orotidine 5'- phosphate decarboxylase (ec 4.1.1.23) (ompdecase)]. [swissprot;acc:p11172] Ranked 224.434 235.583 1.04968
    756 CLPTM1 cleft lip and palate associated transmembrane protein 1. [refseq;acc:nm_001294]
    PAPD5 topoisomerase-related function protein 4-2. [refseq;acc:nm_022447] Measured 4725.28 5261.06 1.11339
    PRKAG2 5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0] Rooted 66.9737 71.4637 1.06704
    TLE4 transducin-like enhancer protein 4. [swissprot;acc:q04727] Squared 31298 36502 1.16627
    757 BPI bactericidal permeability-increasing protein precursor (bpi) (cap 57). [swissprot;acc:p17213] Ranked 224.434 235.583 1.04968
    SF3A2 splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428] Squared 20248.9 23608.3 1.16591
    SRP68 signal recognition particle 68 kda protein (srp68). [swissprot;acc:q9uhb9] Measured 5622.89 6260.02 1.11331
    UQCRC1 ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930] Rooted 60.4457 64.4918 1.06694
    758 KLF5 krueppel-like factor 5 (intestinal-enriched krueppel-like factor) (colon krueppel-like factor) (transcription factor bteb2) (basic transcription element binding protein 2) (bte-binding protein 2) (gc box binding protein 2). [swissprot;acc:q13887] Squared 20248.9 23608.3 1.16591
    PLTP phospholipid transfer protein precursor (lipid transfer protein ii). [swissprot;acc:p55058] Ranked 224.434 235.583 1.04968
    POLE2 dna polymerase epsilon subunit b (ec 2.7.7.7) (dna polymerase ii subunit b). [swissprot;acc:p56282] Measured 3760.3 4185.82 1.11316
    TRMU trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648] Rooted 96.6463 103.103 1.06681
    759 no value nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594] 66.9416 71.4055 1.06668
    COPA coatomer alpha subunit (alpha-coat protein) (alpha-cop) (hepcop) (hep-cop) [contains: xenin (xenopsin-related peptide); proxenin]. [swissprot;acc:p53621] Squared 49280.5 42272.7 1.16578
    OSTF1 osteoclast stimulating factor 1. [swissprot;acc:q92882] Ranked 231.809 243.289 1.04952
    PFKP 6-phosphofructokinase, type c (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme c) (pfk-c) (6-phosphofructokinase, platelet type). [swissprot;acc:q01813] Measured 4254.62 4736.03 1.11315
    760 ATP6V0D2 atpase, h+ transporting, lysosomal 38kda, v0 subunit d isoform 2. [refseq;acc:nm_152565] 5870.2 6533.39 1.11298
    DIRAS1 small gtp-binding tumor suppressor 1. [refseq;acc:nm_145173] Rooted 66.9397 71.4023 1.06667
    NAT10 upf0202 protein kiaa1709. [swissprot;acc:q9h0a0] Ranked 246.055 234.458 1.04946
    RPUSD2 c18b11 homolog (44.9kd). [refseq;acc:nm_152260] Squared 21186.4 24698.3 1.16576
    761 no value alpha-nac protein. [sptrembl;acc:q9h009] Rooted 66.9404 71.4035 1.06667
    CBLB signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191] Ranked 213.325 203.303 1.0493
    EIF5B translation initiation factor if-2. [swissprot;acc:o60841] Measured 5811.51 6467.62 1.1129
    TMBIM4 z-protein (protein cgi-119) (s1r protein). [swissprot;acc:q9hc24] Squared 21186.4 24698.3 1.16576
    762 CBL cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681] Ranked 213.256 203.237 1.0493
    DIRAS2 di-ras2. [refseq;acc:nm_017594] Rooted 66.9397 71.4022 1.06666
    PMS2 pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278] Measured 6231.31 6933.9 1.11275
    TMBIM1 pp1201 protein. [refseq;acc:nm_022152] Squared 21186.4 24698.3 1.16576
    763 DR1 tata-binding protein-associated phosphoprotein (down-regulator of transcription 1) (dr1 protein). [swissprot;acc:q01658] Rooted 60.3269 64.3387 1.0665
    FAIM2 lifeguard; kiaa0950 protein. [refseq;acc:nm_012306] Squared 21186.4 24698.3 1.16576

    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/