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 64574 to 64623 of 66312 in total
    Interaction Map  : Low confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		Network Comparison Type
    		red
    		green
    		network_comparison
    4844 IBTK inhibitor of bruton's tyrsoine kinase; btk-binding protein. [refseq;acc:nm_015525] Measured Divided 8463.74 8544.71 1.00957
    SH3GLB2 sh3-containing protein sh3glb2; sh3-domain, grb2-like, endophilin b2. [refseq;acc:nm_020145] Rooted Subtracted 70.9196 71.9002 0.9806
    SLMO1 erythroid differentiation and denucleation factor 1. [swissprot;acc:o60584] Ranked Divided 203.909 203.244 1.00327
    4845 ARHGEF5 rho guanine nucleotide exchange factor 5 (guanine nucleotide regulatory protein tim) (oncogene tim) (p60 tim) (transforming immortalized mammary oncogene). [swissprot;acc:q12774] Measured 9065.96 8980.16 1.00955
    CYP3A7 cytochrome p450 3a7 (ec 1.14.14.1) (cypiiia7) (p450-hfla). [swissprot;acc:p24462] Squared Subtracted 46592.3 46245.5 346.8
    GNG12 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] Measured 6915.31 6990.74 75.43
    KNG1 kininogen precursor (alpha-2-thiol proteinase inhibitor) [contains: bradykinin]. [swissprot;acc:p01042] Rooted Divided 70.9553 71.9358 1.01382
    OSBPL5 oxysterol binding protein-related protein 5 (osbp-related protein 5) (orp-5). [swissprot;acc:q9h0x9] Squared 45545.5 45920.5 1.00823
    RAF1 raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] Ranked Subtracted 184.241 183.601 0.64
    SH3GLB1 sh3-containing protein sh3glb1; sh3-containing protein sh3glb1; cgi-61 protein; endophilin b1; endophilin b1; bax-interacting factor 1; sh3-domain, grb2-like, endophilin b1. [refseq;acc:nm_016009] Rooted 70.9196 71.9002 0.9806
    SLMO2 protein c20orf45 (cgi-107). [swissprot;acc:q9y3b1] Ranked Divided 203.909 203.244 1.00327
    4846 ARAF a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] Subtracted 184.234 183.595 0.639
    BMP7 bone morphogenetic protein 7 precursor (bmp-7) (osteogenic protein 1) (op-1). [swissprot;acc:p18075] Squared Divided 44928.8 44566 1.00814
    FABP7 fatty acid-binding protein, brain (b-fabp) (brain lipid-binding protein) (blbp) (mammary derived growth inhibitor related). [swissprot;acc:o15540] Rooted 74.314 75.3405 1.01381
    GADD45GIP1 papillomavirus l2 interacting nuclear protein 1; ckii beta binding protein 2; cr6 interacting factor 1; p53-responsive gene 6. [refseq;acc:nm_052850] Ranked 210.422 211.109 1.00326
    GIPC1 rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908] Squared Subtracted 47739.8 48086.3 346.5
    KNG1 kininogen precursor (alpha-2-thiol proteinase inhibitor) [contains: bradykinin]. [swissprot;acc:p01042] Rooted 70.9553 71.9358 0.9805
    LGTN ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214] Measured 7166.16 7240.99 74.83
    SMAD2 mothers against decapentaplegic homolog 2 (smad 2) (mothers against dpp homolog 2) (mad-related protein 2) (hmad-2) (jv18-1) (hsmad2). [swissprot;acc:q15796] Divided 8230.31 8308.86 1.00954
    4847 no value intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3] Ranked 178.257 178.834 1.00324
    BMP5 bone morphogenetic protein 5 precursor (bmp-5). [swissprot;acc:p22003] Squared 44917.8 44555.7 1.00813
    CYP4A22 dj18d14.4 (cytochrome p450, subfamily iva, polypeptide 11). [sptrembl;acc:q9ntl5] Subtracted 47246.9 47589.6 342.7
    HOOK2 hook2 protein. [refseq;acc:nm_013312] Measured Divided 8474.95 8555.81 1.00954
    NUP107 nuclear pore complex protein nup107 (nucleoporin nup107) (107 kda nucleoporin). [swissprot;acc:p57740] Subtracted 8284.03 8358.63 74.6
    PIGC phosphatidylinositol n-acetylglucosaminyltransferase subunit c (ec 2.4.1.198) (phosphatidylinositol-glycan biosynthesis, class c protein) (pig-c). [swissprot;acc:q92535] Rooted Divided 70.3657 71.3373 1.01381
    POU3F2 pou domain, class 3, transcription factor 2 (nervous-system specific octamer-binding transcription factor n-oct-3) (brain-specific homeobox/pou domain protein 2) (brain-2) (brn-2 protein). [swissprot;acc:p20265] Subtracted 73.2993 74.2778 0.9785
    ZNF394 zinc finger protein 99. [refseq;acc:nm_032164] Ranked 206.472 205.839 0.633
    4848 no value myo-inositol 1-phosphate synthase a1. [refseq;acc:nm_016368] Divided 203.884 203.239 1.00317
    pou domain, class 3, transcription factor 3 (brain-specific homeobox/pou domain protein 1) (brain-1) (brn-1 protein). [swissprot;acc:p20264] Rooted Subtracted 73.2993 74.2778 0.9785
    BMP8A bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [swissprot;acc:p34820] Squared Divided 44910.2 44548.6 1.00812
    FBXL11 f-box and leucine-rich repeat protein 11; f-box protein fbl11. [refseq;acc:nm_012308] Measured Subtracted 7399.95 7474.27 74.32
    HOOK1 hook1 protein. [refseq;acc:nm_015888] Divided 8475.45 8556.21 1.00953
    RPL5 60s ribosomal protein l5. [swissprot;acc:p46777] Rooted 69.0542 70.0063 1.01379
    SDC3 syndecan-3 (synd3). [swissprot;acc:o75056] Squared Subtracted 53479.3 53139.6 339.7
    ZSCAN12 zinc finger protein 305. [swissprot;acc:o43309] Ranked 206.479 205.846 0.633
    4849 no value germ cell-less. [refseq;acc:nm_022471] 208.276 208.904 0.628
    BMP6 bone morphogenetic protein 6 precursor (bmp-6). [swissprot;acc:p22004] Squared Divided 44916.6 44554.6 1.00812
    COMP cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] Measured Subtracted 7226.62 7300.69 74.07
    CYP4A11 cytochrome p450 4a11 precursor (ec 1.14.15.3) (cypiva11) (fatty acid omega-hydroxylase) (p-450 hk omega) (lauric acid omega-hydroxylase) (cyp4aii) (p450-hl-omega). [swissprot;acc:q02928] Squared 47238 47576.6 338.6
    HRBL hiv-1 rev binding protein-like; rev/rex activation domain binding protein-related. [refseq;acc:nm_006076] Measured Divided 8464.11 8544.68 1.00952
    LARS2 probable leucyl-trna synthetase, mitochondrial precursor (ec 6.1.1.4) (leucine--trna ligase) (leurs). [swissprot;acc:q15031] Rooted 76.1787 77.2177 1.01364
    SPARCL1 sparc-like protein 1 precursor (high endothelial venule protein) (hevin) (mast 9). [swissprot;acc:q14515] Subtracted 73.2993 74.2778 0.9785
    ZNF394 zinc finger protein 99. [refseq;acc:nm_032164] Ranked Divided 206.472 205.839 1.00308
    4850 CYP3A5 cytochrome p450 3a5 (ec 1.14.14.1) (cypiiia5) (p450-pcn3). [swissprot;acc:p20815] Squared Subtracted 46609.5 46272.1 337.4
    EIF1B protein translation factor sui1 homolog gc20. [swissprot;acc:o60739] Ranked 205.448 206.075 0.627
    HOOK3 golgi-associated microtubule-binding protein hook3; hook3 protein. [refseq;acc:nm_032410] Measured Divided 8477.6 8557.97 1.00948
    PHKG2 phosphorylase b kinase gamma catalytic chain, testis/liver isoform (ec 2.7.1.38) (phk-gamma-t) (phosphorylase kinase gamma subunit 2) (psk-c3). [swissprot;acc:p15735] Rooted 64.5419 63.6803 1.01353
    SPARC sparc precursor (secreted protein acidic and rich in cysteine) (osteonectin) (on) (basement membrane protein bm-40). [swissprot;acc:p09486] Subtracted 73.2993 74.2778 0.9785
    THBS3 thrombospondin 3 precursor. [swissprot;acc:p49746] Measured 7226.69 7300.73 74.04
    XPO1 exportin 1; exportin-1 (required for chromosome region maintenance); exportin 1 (crm1, yeast, homolog); crm1, yeast, homolog. [refseq;acc:nm_003400] Squared Divided 48323.1 47936 1.00808

    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/