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 2608 to 2657 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Value Type
    		red
    		green
    		network_comparison
    652 tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [refseq;acc:nm_014886] Ranked 248.994 235.255 1.0584
    653 arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069] Rooted 64.4927 69.539 1.07825
    dok-like protein. [refseq;acc:nm_024872] Ranked 216.504 204.622 1.05807
    methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192] Measured 5560.06 6248.27 1.12378
    testis-specific chromodomain protein y protein 2. [swissprot;acc:q9y6f7] Squared 29012.4 34164 1.17757
    654 docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496] Ranked 216.504 204.622 1.05807
    histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351] Measured 4088.63 4593.43 1.12346
    peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [swissprot;acc:o14936] Rooted 59.9021 64.5838 1.07816
    sprouty homolog 4 (spry-4). [swissprot;acc:q9c004] Squared 27174.1 31992.4 1.17731
    655 dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9] Measured 4088.63 4593.43 1.12346
    docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704] Ranked 216.504 204.622 1.05807
    hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [refseq;acc:nm_152794] Rooted 59.9021 64.5838 1.07816
    sprouty homolog 3 (spry-3). [swissprot;acc:o43610] Squared 27174.1 31992.4 1.17731
    656 apolipoprotein a-i binding protein; apoa-i binding protein. [refseq;acc:nm_144772] Measured 6139.04 6893.7 1.12293
    single-minded homolog 1. [swissprot;acc:p81133] Rooted 59.9021 64.5838 1.07816
    sprouty homolog 1 (spry-1) (fragment). [swissprot;acc:o43609] Squared 27174.1 31992.4 1.17731
    tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685] Ranked 216.504 204.622 1.05807
    657 rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908] Measured 6079.26 6824.47 1.12258
    sprouty homolog 2 (spry-2). [swissprot;acc:o43597] Squared 27174.1 31992.4 1.17731
    synapsin iii. [swissprot;acc:o14994] Ranked 229.072 216.576 1.0577
    vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504] Rooted 64.75 69.8065 1.07809
    658 apical-like protein (apxl protein). [swissprot;acc:q13796] Measured 6088.77 6834.87 1.12254
    aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468] Ranked 229.072 216.576 1.0577
    eukaryotic translation initiation factor 3 subunit 9 (eif-3 eta) (eif3 p116) (eif3 p110) (eif3b). [swissprot;acc:p55884] Rooted 52.7523 56.8686 1.07803
    similar to trna synthetase class ii. [refseq;acc:nm_152268] Squared 22293.8 26242.6 1.17713
    659 28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933] Rooted 51.7081 47.9816 1.07767
    hairy/enhancer-of-split related with yrpw motif 1 (hairy and enhancer of split related-1) (hesr-1) (cardiovascular helix-loop-helix factor 2) (hes-related repressor protein 2 herp2). [swissprot;acc:q9y5j3] Ranked 229.072 216.576 1.0577
    ornithine carbamoyltransferase, mitochondrial precursor (ec 2.1.3.3) (otcase) (ornithine transcarbamylase). [swissprot;acc:p00480] Squared 24614 28973.4 1.17711
    shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859] Measured 6089.21 6835.34 1.12253
    660 actin binding lim protein 2. [refseq;acc:nm_032432] Ranked 229.072 216.576 1.0577
    fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] Rooted 133.216 123.627 1.07756
    nadh-ubiquinone oxidoreductase b22 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b22) (ci-b22). [swissprot;acc:q9y6m9] Squared 33024.9 38867.8 1.17692
    u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695] Measured 5575.18 6254.85 1.12191
    661 delta-aminolevulinic acid dehydratase (ec 4.2.1.24) (porphobilinogen synthase) (aladh). [swissprot;acc:p13716] Squared 22223.1 26152.4 1.17681
    hairy/enhancer-of-split related with yrpw motif-like. [refseq;acc:nm_014571] Ranked 229.072 216.576 1.0577
    nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4] Rooted 68.8243 74.1496 1.07738
    step ii splicing factor slu7. [refseq;acc:nm_006425] Measured 5575.18 6254.85 1.12191
    662 nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [swissprot;acc:q9h4d5] Rooted 68.8237 74.1484 1.07737
    partitioning defective-6 homolog gamma (par-6 gamma) (par6d). [swissprot;acc:q9byg4] Measured 6374.65 7145.59 1.12094
    synapsin ii. [swissprot;acc:q92777] Ranked 229.072 216.576 1.0577
    ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855] Squared 23947.4 28163.7 1.17607
    663 acrc protein; putative nuclear protein. [refseq;acc:nm_052957] 23947.7 28163.9 1.17606
    mitochondrial ribosome recycling factor. [refseq;acc:nm_138777] Ranked 229.072 216.576 1.0577
    nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [swissprot;acc:q9ubu9] Rooted 68.8197 74.1413 1.07733
    tubby protein homolog. [swissprot;acc:p50607] Measured 6374.65 7145.59 1.12094
    664 neuroepithelial cell transforming gene 1; guanine nucleotide regulatory protein (oncogene); rho guanine nucleotide exchange factor (gef) 8. [refseq;acc:nm_005863] Rooted 51.6042 55.574 1.07693
    peroxisomal targeting signal 1 receptor (peroxismore receptor 1) (peroxisomal c-terminal targeting signal import receptor) (pts1-bp) (peroxin-5) (pts1 receptor). [swissprot;acc:p50542] Ranked 229.072 216.576 1.0577
    protein kinase c, iota type (ec 2.7.1.37) (npkc-iota) (atypical protein kinase c-lamda/iota) (apkc-lambda/iota). [swissprot;acc:p41743] Measured 6374.65 7145.59 1.12094
    ubiquitin-like protein smt3a. [swissprot;acc:p55854] Squared 23948 28164.1 1.17605
    665 hairy/enhancer-of-split related with yrpw motif 2; gridlock; hes-related repressor protein 1. [refseq;acc:nm_012259] Ranked 229.072 216.576 1.0577

    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/