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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 4808 to 4857 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Value Type
    		red
    		green
    		network_comparison
    1202 skeletal muscle tropomodulin (sk-tmod) (tropomodulin 4). [swissprot;acc:q9nzq9] Squared 19317.7 21958.6 1.13671
    1203 geranylgeranyl pyrophosphate synthetase (ggpp synthetase) (ggppsase) (geranylgeranyl diphosphate synthase) [includes: dimethylallyltransferase (ec 2.5.1.1); geranyltranstransferase (ec 2.5.1.10); farnesyltranstransferase (ec 2.5.1.29)]. [swissprot;acc:o95749] Measured 4322.65 4696.04 1.08638
    myb-related protein a (a-myb). [swissprot;acc:p10243] Rooted 60.1161 62.9033 1.04636
    tumor necrosis factor, alpha-induced protein 1, endothelial (b12 protein). [swissprot;acc:q13829] Ranked 219.023 213.606 1.02536
    ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [swissprot;acc:q9nyl9] Squared 19317.7 21958.6 1.13671
    1204 polymerase delta-interacting protein 1; tnfaip1-like. [refseq;acc:nm_178863] Ranked 219.022 213.607 1.02535
    protein ad-016 (protein cgi-116) (x0009). [swissprot;acc:q9y3c0] Rooted 63.2865 66.2117 1.04622
    suppressor of cytokine signaling 1 (socs-1) (jak-binding protein) (jab) (stat induced stat inhibitor 1) (ssi-1) (tec-interacting protein 3) (tip-3). [swissprot;acc:o15524] Measured 5946.33 6459.79 1.08635
    tropomodulin 1 (erythrocyte tropomodulin) (e-tmod). [swissprot;acc:p28289] Squared 19317.7 21958.6 1.13671
    1205 glia maturation factor gamma (gmf-gamma). [swissprot;acc:o60234] Measured 5946.33 6459.79 1.08635
    ny-ren-62 antigen (fragment). [sptrembl;acc:q9y590] Ranked 224.805 219.251 1.02533
    protein kinase clk2 (ec 2.7.1.-) (cdc-like kinase 2). [swissprot;acc:p49760] Rooted 64.7548 67.7419 1.04613
    sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [swissprot;acc:q9y5x1] Squared 19317.7 21958.6 1.13671
    1206 asc-1 complex subunit p100. [refseq;acc:nm_032204] Measured 5946.33 6459.79 1.08635
    integral membrane protein cii-3b. [sptrembl;acc:o75609] Ranked 207.646 212.891 1.02526
    neuronal tropomodulin (n-tmod) (tropomodulin 2). [swissprot;acc:q9nzr1] Squared 19317.7 21958.6 1.13671
    similar to lim domain only 7 (fragment). [sptrembl;acc:q8n6m2] Rooted 62.5668 65.4521 1.04612
    1207 fk506-binding protein 1a (ec 5.2.1.8) (peptidyl-prolyl cis-trans isomerase) (ppiase) (rotamase) (12 kda fkbp) (fkbp-12) (immunophilin fkbp12). [swissprot;acc:p20071] Measured 5946.33 6459.79 1.08635
    homeobox protein dlx-2. [swissprot;acc:q07687] Squared 19317.7 21958.6 1.13671
    p10-binding protein. [refseq;acc:nm_024491] Rooted 60.7029 63.5018 1.04611
    succinate dehydrogenase cytochrome b560 subunit, mitochondrial precursor (integral membrane protein cii-3) (qps1) (qps-1) (succinate dehydrogenase complex subunit c) (succinate-ubiquinone oxidoreductase cytochrome b large subunit) (cybl). [swissprot;acc:q99643] Ranked 207.644 212.888 1.02525
    1208 homeobox protein dlx-5. [swissprot;acc:p56178] Squared 19317.7 21958.6 1.13671
    meiotic recombination protein dmc1/lim15 homolog. [swissprot;acc:q14565] Measured 5913.73 6423.98 1.08628
    protein kinase clk3 (ec 2.7.1.-) (cdc-like kinase 3). [swissprot;acc:p49761] Rooted 64.7526 67.7372 1.04609
    signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240] Ranked 224.878 219.342 1.02524
    1209 bifunctional aminoacyl-trna synthetase [includes: glutamyl-trna synthetase (ec 6.1.1.17) (glutamate--trna ligase); prolyl-trna synthetase (ec 6.1.1.15) (proline--trna ligase)]. [swissprot;acc:p07814] Measured 5420.87 5887.53 1.08609
    fetal brain protein 239 (239fb). [swissprot;acc:q15777] Squared 19317.7 21958.6 1.13671
    homeobox protein six1 (sine oculis homeobox homolog 1). [swissprot;acc:q15475] Rooted 61.3914 64.2183 1.04605
    succinate dehydrogenase [ubiquinone] iron-sulfur protein, mitochondrial precursor (ec 1.3.5.1) (ip) (iron-sulfur subunit of complex ii). [swissprot;acc:p21912] Ranked 207.931 213.175 1.02522
    1210 homeobox protein dlx-3. [swissprot;acc:o60479] Squared 19317.7 21958.6 1.13671
    kinesin-like protein kif2 (kinesin-2) (hk2). [swissprot;acc:o00139] Ranked 224.764 219.241 1.02519
    proliferation-associated protein 2g4 (cell cycle protein p38-2g4 homolog) (hg4-1). [swissprot;acc:q9uq80] Rooted 61.3876 64.2125 1.04602
    trimethyllysine dioxygenase, mitochondrial precursor (ec 1.14.11.8) (epsilon-trimethyllysine 2-oxoglutarate dioxygenase) (tml-alpha- ketoglutarate dioxygenase) (tml hydroxylase) (tml dioxygenase) (tmld). [swissprot;acc:q9nvh6] Measured 6410.73 6962.22 1.08603
    1211 activated p21cdc42hs kinase. [refseq;acc:nm_005781] Squared 19317.7 21958.6 1.13671
    chromosome 11 open reading frame2; chromosome 11 open reading frame2. [refseq;acc:nm_013265] Ranked 214.364 219.759 1.02517
    dna topoisomerase ii, alpha isozyme (ec 5.99.1.3). [swissprot;acc:p11388] Rooted 67.2521 70.3462 1.04601
    gtp-binding protein era homolog (hera) (fragment). [swissprot;acc:o75616] Measured 6410.73 6962.22 1.08603
    1212 hiv-1 rev binding protein 2; rev interacting protein. [refseq;acc:nm_007043] 4077.89 4428.28 1.08592
    homeobox protein six2 (sine oculis homeobox homolog 2). [swissprot;acc:q9npc8] Rooted 61.3832 64.2055 1.04598
    kinesin-like protein kif13a (kinesin-like protein rbkin). [swissprot;acc:q9h1h9] Ranked 214.364 219.759 1.02517
    mitogen-activated protein kinase kinase kinase 7 interacting protein 2 isoform 1; tak1-binding protein 2. [refseq;acc:nm_015093] Squared 19317.7 21958.6 1.13671
    1213 40s ribosomal protein s8. [swissprot;acc:p09058] Rooted 61.4774 64.3044 1.04598
    branched-chain amino acid aminotransferase, cytosolic (ec 2.6.1.42) (bcat(c)) (eca39 protein). [swissprot;acc:p54687] Measured 5890.62 6396.53 1.08588
    conserved oligomeric golgi complex component 2 (low density lipoprotein receptor defect c-complementing protein). [swissprot;acc:q14746] Ranked 214.364 219.759 1.02517
    ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [swissprot;acc:q06546] Squared 20823.1 23668.4 1.13664
    1214 dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880] Rooted 67.2519 70.3434 1.04597
    ga binding protein beta-2 chain (gabp-beta-2 subunit) (transcription factor e4tf1-47) (gapbp-2) (nuclear respiratory factor-2 subunit gamma). [swissprot;acc:q06545] Squared 20823.1 23668.4 1.13664
    kinesin-like protein kif13b (kinesin-like protein gakin). [swissprot;acc:q9nqt8] Ranked 214.364 219.759 1.02517
    mitogen-activated protein kinase kinase kinase 7 (ec 2.7.1.-) (transforming growth factor-beta-activated kinase 1) (tgf-beta- activated kinase 1). [swissprot;acc:o43318] Measured 6001.16 6515.9 1.08577
    1215 branched-chain amino acid aminotransferase, mitochondrial precursor (ec 2.6.1.42) (bcat(m)) (placental protein 18) (pp18). [swissprot;acc:o15382] 5892.05 6397.28 1.08575

    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
    - 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/