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 Network Comparison Type Value Type description Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 64474 to 64523 of 66312 in total
    Interaction Map  : Low confidence
    Filtered  : 1
    Rank
    		Hugo
    		Network Comparison Type
    		Value Type
    		description
    		red
    		green
    		network_comparison
    4832 FBXL10 Divided Measured protein containing cxxc domain 2. [refseq;acc:nm_032590] 7397.17 7470.36 1.00989
    GOLPH3 Rooted golgi phosphoprotein 3; golgi protein; golgi peripheral membrane protein 1, 34 kda; golgi-associated protein; coat-protein. [refseq;acc:nm_022130] 72.3859 73.4102 1.01415
    MAGI1 Subtracted Ranked bai1-associated protein 1; ww domain-containing protein 3; atrophin-1 interacting protein 3. [refseq;acc:nm_004742] 204.514 203.783 0.731
    NIN Squared ninein (gsk3b interacting protein). [refseq;acc:nm_016350] 38969.1 38596 373.1
    RPS16 Divided Ranked 40s ribosomal protein s16. [swissprot;acc:p17008] 208.276 209.034 1.00364
    SMAD1 Subtracted Rooted mothers against decapentaplegic homolog 1 (smad 1) (mothers against dpp homolog 1) (mad-related protein 1) (transforming growth factor- beta signaling protein-1) (bsp-1) (hsmad1) (jv4-1). [swissprot;acc:q15797] 70.2394 71.2351 0.9957
    WAS Divided Squared wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] 45468.9 45083.7 1.00854
    4833 ATP2B3 Measured plasma membrane calcium-transporting atpase 3 (ec 3.6.3.8) (pmca3) (plasma membrane calcium pump isoform 3) (plasma membrane calcium atpase isoform 3). [swissprot;acc:q16720] 8308 8390.13 1.00989
    COMP Subtracted Rooted cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] 67.1182 68.1139 0.9957
    GNG5 Measured guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] 6935.03 7015.07 80.04
    GP5 Divided Ranked platelet glycoprotein v precursor (gpv) (cd42d). [swissprot;acc:p40197] 184.376 183.71 1.00363
    H2AFZ Subtracted histone h2a.z (h2a/z). [swissprot;acc:p17317] 203.113 203.823 0.71
    PELI2 Divided Rooted pellino 2. [refseq;acc:nm_021255] 70.329 71.3191 1.01408
    TFAP2A Squared transcription factor ap-2 alpha (ap2-alpha) (activating enhancer- binding protein 2 alpha) (ap-2 transcription factor) (activator protein-2) (ap-2). [swissprot;acc:p05549] 46895.6 46499 1.00853
    TMEM115 Subtracted pl6 protein (placental protein 6). [swissprot;acc:q12893] 47834.7 48207.3 372.6
    4834 no value Divided Rooted pellino protein. [refseq;acc:nm_020651] 70.3293 71.3184 1.01406
    BRAF Subtracted Ranked b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056] 184.583 183.88 0.703
    CPN2 Divided carboxypeptidase n 83 kda chain (carboxypeptidase n regulatory subunit) (fragment). [swissprot;acc:p22792] 184.376 183.711 1.00362
    CYP27B1 Squared 25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [swissprot;acc:o15528] 15514.2 15383 1.00853
    GNG8 Subtracted Measured guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] 6934.19 7014.03 79.84
    LAPTM4A Squared lysosomal-associated transmembrane protein 4a (golgi 4-transmembrane spanning transporter mtp). [swissprot;acc:q15012] 47834.7 48207.3 372.6
    RACGAP1 Divided Measured rac gtpase activating protein 1; gtpase activating protein. [refseq;acc:nm_013277] 8173.79 8253.49 1.00975
    THBS3 Subtracted Rooted thrombospondin 3 precursor. [swissprot;acc:p49746] 67.1186 68.114 0.9954
    4835 EDEM2 Divided Squared putative alpha-mannosidase c20orf31 precursor (ec 3.2.1.-). [swissprot;acc:q9bv94] 41735.1 41382.3 1.00853
    GNG8 Subtracted Rooted guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] 66.93 65.9368 0.9932
    IGBP1 Ranked immunoglobulin-binding protein 1 (cd79a-binding protein 1) (b cell signal transduction molecule alpha 4) (alpha 4 protein). [swissprot;acc:p78318] 199.078 198.388 0.69
    LAPTM4B Squared lysosomal-associated transmembrane protein 4 beta; putative integral membrane transporter. [refseq;acc:nm_018407] 47831.2 48202.8 371.6
    MAGI1 Divided Ranked bai1-associated protein 1; ww domain-containing protein 3; atrophin-1 interacting protein 3. [refseq;acc:nm_004742] 204.514 203.783 1.00359
    PCF11 Measured pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913] 9221.16 9132.72 1.00968
    PELI3 Rooted pellino 3 alpha. [refseq;acc:nm_145065] 70.3295 71.3177 1.01405
    RACGAP1 Subtracted Measured rac gtpase activating protein 1; gtpase activating protein. [refseq;acc:nm_013277] 8173.79 8253.49 79.7
    4836 AP3B1 Divided Ranked adapter-related protein complex 3 beta 1 subunit (beta-adaptin 3a) (ap-3 complex beta-3a subunit) (beta-3a-adaptin). [swissprot;acc:o00203] 209.715 210.462 1.00356
    ARF5 Measured adp-ribosylation factor 5. [swissprot;acc:p26437] 8859.58 8944.85 1.00962
    GADD45GIP1 Subtracted Ranked papillomavirus l2 interacting nuclear protein 1; ckii beta binding protein 2; cr6 interacting factor 1; p53-responsive gene 6. [refseq;acc:nm_052850] 210.422 211.109 0.687
    GNG3 Measured guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] 6932.11 7011.46 79.35
    GNG5 Rooted guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] 66.9343 65.9439 0.9904
    HMG20B Squared high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339] 38880.7 38510.7 370
    SLC35D2 Divided Rooted sqv-7-like protein (fragment). [sptrembl;acc:o95454] 70.571 71.5599 1.01401
    TFAP2C Squared transcription factor ap-2 gamma (ap2-gamma) (activating enhancer- binding protein 2 gamma) (transcription factor erf-1). [swissprot;acc:q92754] 46895.6 46499 1.00853
    4837 no value Subtracted Ranked ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] 179.602 178.915 0.687
    CIAO1 Squared wd-repeat containing protein ciao 1. [swissprot;acc:o76071] 47623.2 47258.5 364.7
    CTRL Divided Rooted 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] 72.0817 73.0839 1.0139
    GNG4 Subtracted Measured guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] 6931.71 7010.97 79.26
    H2AFZ Divided Ranked histone h2a.z (h2a/z). [swissprot;acc:p17317] 203.113 203.823 1.0035
    HRB Measured nucleoporin-like protein rip (hiv-1 rev-binding protein) (rev interacting protein) (rev/rex activation domain-binding protein). [swissprot;acc:p52594] 8463.46 8544.73 1.0096
    PELI2 Subtracted Rooted pellino 2. [refseq;acc:nm_021255] 70.329 71.3191 0.9901
    TFAP2B Divided Squared transcription factor ap-2 beta (ap2-beta) (activating enhancer-binding protein 2 beta). [swissprot;acc:q92481] 46895.6 46499 1.00853
    4838 no value Subtracted Rooted pellino protein. [refseq;acc:nm_020651] 70.3293 71.3184 0.9891
    CDC6 Ranked cdc6 homolog; cdc18 (cell division cycle 18, s.pombe, homolog)-like; cdc6-related protein. [refseq;acc:nm_001254] 198.263 197.58 0.683
    CYP3A4 Squared cytochrome p450 3a4 (ec 1.14.13.67) (quinine 3-monooxygenase) (cypiiia4) (nifedipine oxidase) (nf-25) (p450-pcn1). [swissprot;acc:p08684] 46568.5 46204.8 363.7

    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/