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 description Gene Network Comparison Type Hugo Value Type red Interaction Map Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 3025 to 3074 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Value Type
    		red
    		green
    		network_comparison
    757 bactericidal permeability-increasing protein precursor (bpi) (cap 57). [swissprot;acc:p17213] BPI Ranked 224.434 235.583 1.04968
    signal recognition particle 68 kda protein (srp68). [swissprot;acc:q9uhb9] SRP68 Measured 5622.89 6260.02 1.11331
    splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428] SF3A2 Squared 20248.9 23608.3 1.16591
    ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930] UQCRC1 Rooted 60.4457 64.4918 1.06694
    758 dna polymerase epsilon subunit b (ec 2.7.7.7) (dna polymerase ii subunit b). [swissprot;acc:p56282] POLE2 Measured 3760.3 4185.82 1.11316
    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] KLF5 Squared 20248.9 23608.3 1.16591
    phospholipid transfer protein precursor (lipid transfer protein ii). [swissprot;acc:p55058] PLTP Ranked 224.434 235.583 1.04968
    trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648] TRMU Rooted 96.6463 103.103 1.06681
    759 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] PFKP Measured 4254.62 4736.03 1.11315
    coatomer alpha subunit (alpha-coat protein) (alpha-cop) (hepcop) (hep-cop) [contains: xenin (xenopsin-related peptide); proxenin]. [swissprot;acc:p53621] COPA Squared 49280.5 42272.7 1.16578
    nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594] no value Rooted 66.9416 71.4055 1.06668
    osteoclast stimulating factor 1. [swissprot;acc:q92882] OSTF1 Ranked 231.809 243.289 1.04952
    760 atpase, h+ transporting, lysosomal 38kda, v0 subunit d isoform 2. [refseq;acc:nm_152565] ATP6V0D2 Measured 5870.2 6533.39 1.11298
    c18b11 homolog (44.9kd). [refseq;acc:nm_152260] RPUSD2 Squared 21186.4 24698.3 1.16576
    small gtp-binding tumor suppressor 1. [refseq;acc:nm_145173] DIRAS1 Rooted 66.9397 71.4023 1.06667
    upf0202 protein kiaa1709. [swissprot;acc:q9h0a0] NAT10 Ranked 246.055 234.458 1.04946
    761 alpha-nac protein. [sptrembl;acc:q9h009] no value Rooted 66.9404 71.4035 1.06667
    signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191] CBLB Ranked 213.325 203.303 1.0493
    translation initiation factor if-2. [swissprot;acc:o60841] EIF5B Measured 5811.51 6467.62 1.1129
    z-protein (protein cgi-119) (s1r protein). [swissprot;acc:q9hc24] TMBIM4 Squared 21186.4 24698.3 1.16576
    762 cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681] CBL Ranked 213.256 203.237 1.0493
    di-ras2. [refseq;acc:nm_017594] DIRAS2 Rooted 66.9397 71.4022 1.06666
    pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278] PMS2 Measured 6231.31 6933.9 1.11275
    pp1201 protein. [refseq;acc:nm_022152] TMBIM1 Squared 21186.4 24698.3 1.16576
    763 6-phosphofructokinase, muscle type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme a) (pfk-a) (phosphofructokinase-m). [swissprot;acc:p08237] PFKM Measured 4250.54 4729.67 1.11272
    lifeguard; kiaa0950 protein. [refseq;acc:nm_012306] FAIM2 Squared 21186.4 24698.3 1.16576
    putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [swissprot;acc:q9y5n5] N6AMT1 Ranked 228.78 218.091 1.04901
    tata-binding protein-associated phosphoprotein (down-regulator of transcription 1) (dr1 protein). [swissprot;acc:q01658] DR1 Rooted 60.3269 64.3387 1.0665
    764 6-phosphofructokinase, liver type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme b) (pfk-b). [swissprot;acc:p17858] PFKL Measured 4250.18 4729.12 1.11269
    cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520] CBS Rooted 63.5181 67.7402 1.06647
    sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772] no value Squared 21186.4 24698.3 1.16576
    u4/u6-associated rna splicing factor. [refseq;acc:nm_004698] PRPF3 Ranked 222.082 211.707 1.04901
    765 hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [swissprot;acc:q9y5r4] HEMK1 229.045 218.343
    polymerase (dna directed) sigma; topoisomerase-related function protein 4-1; polymerase (dna-directed) sigma. [refseq;acc:nm_006999] POLS Measured 4726.38 5258.95 1.11268
    sterol regulatory element binding protein-1 (srebp-1) (sterol regulatory element-binding transcription factor 1). [swissprot;acc:p36956] SREBF1 Squared 21186.4 24698.3 1.16576
    transforming protein rhoc (h9). [swissprot;acc:p08134] RHOC Rooted 63.5181 67.7402 1.06647
    766 atp synthase gamma chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p36542] ATP5C1 Squared 24509.4 28571.6 1.16574
    protein tara (trio-associated repeat on actin) (hrihfb2122). [swissprot;acc:q9h2d6] TRIOBP Ranked 213.804 224.226 1.04875
    thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762] TST Rooted 63.5181 67.7402 1.06647
    ubiquitin-conjugating enzyme e2 variant 1 isoform b; dna-binding protein. [refseq;acc:nm_003349] TMEM189 Measured 6691.93 7445.09 1.11255
    767 3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325] MPST Rooted 63.5181 67.7402 1.06647
    atp synthase oligomycin sensitivity conferral protein, mitochondrial precursor (ec 3.6.3.14) (oscp). [swissprot;acc:p48047] ATP5O Squared 24509.4 28571.6 1.16574
    rho interacting protein 3. [refseq;acc:nm_015134] no value Ranked 213.803 224.224 1.04874
    utp--glucose-1-phosphate uridylyltransferase 2 (ec 2.7.7.9) (udp- glucose pyrophosphorylase 2) (udpgp 2) (ugpase 2). [swissprot;acc:q16851] UGP2 Measured 6691.21 7444.22 1.11254
    768 dnaj homolog subfamily b member 4 (heat shock 40 kda protein 1 homolog) (heat shock protein 40 homolog) (hsp40 homolog). [swissprot;acc:q9udy4] DNAJB4 Ranked 210.946 221.225 1.04873
    eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] EIF5 Squared 12108.4 14114.6 1.16569
    transforming protein rhoa (h12). [swissprot;acc:p06749] RHOA Rooted 63.5181 67.7402 1.06647
    ubiquitin-conjugating enzyme e2 variant 2; 1 alpha,25-dihydroxyvitamin d3-inducible; enterocyte differentiation promoting factor; methyl methanesulfonate sensitive 2, s. cerevisiae, homolog of. [refseq;acc:nm_003350] UBE2V2 Measured 6690.44 7443.29 1.11253
    769 60s ribosomal protein l39. [swissprot;acc:p02404] no value Rooted 55.6817 59.3786 1.06639
    cab2. [refseq;acc:nm_033419] PERLD1 Ranked 210.946 221.225 1.04873

    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/