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 Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2612 to 2661 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		Value Type
    		description
    		red
    		green
    		network_comparison
    653 SORBS2 Rooted arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069] 64.4927 69.539 1.07825
    654 no value Measured histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351] 4088.63 4593.43 1.12346
    Squared sprouty homolog 4 (spry-4). [swissprot;acc:q9c004] 27174.1 31992.4 1.17731
    CASK Rooted peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [swissprot;acc:o14936] 59.9021 64.5838 1.07816
    DOK2 Ranked docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496] 216.504 204.622 1.05807
    655 no value Measured dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9] 4088.63 4593.43 1.12346
    DOK1 Ranked docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704] 216.504 204.622 1.05807
    HIF3A Rooted hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [refseq;acc:nm_152794] 59.9021 64.5838 1.07816
    SPRY3 Squared sprouty homolog 3 (spry-3). [swissprot;acc:o43610] 27174.1 31992.4 1.17731
    656 APOA1BP Measured apolipoprotein a-i binding protein; apoa-i binding protein. [refseq;acc:nm_144772] 6139.04 6893.7 1.12293
    FRK Ranked tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685] 216.504 204.622 1.05807
    SIM1 Rooted single-minded homolog 1. [swissprot;acc:p81133] 59.9021 64.5838 1.07816
    SPRY1 Squared sprouty homolog 1 (spry-1) (fragment). [swissprot;acc:o43609] 27174.1 31992.4 1.17731
    657 GIPC1 Measured rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908] 6079.26 6824.47 1.12258
    SORBS3 Rooted vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504] 64.75 69.8065 1.07809
    SPRY2 Squared sprouty homolog 2 (spry-2). [swissprot;acc:o43597] 27174.1 31992.4 1.17731
    SYN3 Ranked synapsin iii. [swissprot;acc:o14994] 229.072 216.576 1.0577
    658 no value aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468]
    EIF3B Rooted eukaryotic translation initiation factor 3 subunit 9 (eif-3 eta) (eif3 p116) (eif3 p110) (eif3b). [swissprot;acc:p55884] 52.7523 56.8686 1.07803
    PARS2 Squared similar to trna synthetase class ii. [refseq;acc:nm_152268] 22293.8 26242.6 1.17713
    SHROOM2 Measured apical-like protein (apxl protein). [swissprot;acc:q13796] 6088.77 6834.87 1.12254
    659 HEY1 Ranked 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] 229.072 216.576 1.0577
    MRPS9 Rooted 28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933] 51.7081 47.9816 1.07767
    OTC Squared ornithine carbamoyltransferase, mitochondrial precursor (ec 2.1.3.3) (otcase) (ornithine transcarbamylase). [swissprot;acc:p00480] 24614 28973.4 1.17711
    SHROOM3 Measured shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859] 6089.21 6835.34 1.12253
    660 no value u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695] 5575.18 6254.85 1.12191
    ABLIM2 Ranked actin binding lim protein 2. [refseq;acc:nm_032432] 229.072 216.576 1.0577
    FIP1L1 Rooted fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] 133.216 123.627 1.07756
    NDUFB9 Squared nadh-ubiquinone oxidoreductase b22 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b22) (ci-b22). [swissprot;acc:q9y6m9] 33024.9 38867.8 1.17692
    661 ALAD delta-aminolevulinic acid dehydratase (ec 4.2.1.24) (porphobilinogen synthase) (aladh). [swissprot;acc:p13716] 22223.1 26152.4 1.17681
    HEYL Ranked hairy/enhancer-of-split related with yrpw motif-like. [refseq;acc:nm_014571] 229.072 216.576 1.0577
    NXF5 Rooted nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4] 68.8243 74.1496 1.07738
    SLU7 Measured step ii splicing factor slu7. [refseq;acc:nm_006425] 5575.18 6254.85 1.12191
    662 no value Squared ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855] 23947.4 28163.7 1.17607
    NXF3 Rooted nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [swissprot;acc:q9h4d5] 68.8237 74.1484 1.07737
    PARD6G Measured partitioning defective-6 homolog gamma (par-6 gamma) (par6d). [swissprot;acc:q9byg4] 6374.65 7145.59 1.12094
    SYN2 Ranked synapsin ii. [swissprot;acc:q92777] 229.072 216.576 1.0577
    663 ACRC Squared acrc protein; putative nuclear protein. [refseq;acc:nm_052957] 23947.7 28163.9 1.17606
    MRRF Ranked mitochondrial ribosome recycling factor. [refseq;acc:nm_138777] 229.072 216.576 1.0577
    NXF1 Rooted nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [swissprot;acc:q9ubu9] 68.8197 74.1413 1.07733
    TUB Measured tubby protein homolog. [swissprot;acc:p50607] 6374.65 7145.59 1.12094
    664 NET1 Rooted neuroepithelial cell transforming gene 1; guanine nucleotide regulatory protein (oncogene); rho guanine nucleotide exchange factor (gef) 8. [refseq;acc:nm_005863] 51.6042 55.574 1.07693
    PEX5 Ranked peroxisomal targeting signal 1 receptor (peroxismore receptor 1) (peroxisomal c-terminal targeting signal import receptor) (pts1-bp) (peroxin-5) (pts1 receptor). [swissprot;acc:p50542] 229.072 216.576 1.0577
    PRKCI Measured protein kinase c, iota type (ec 2.7.1.37) (npkc-iota) (atypical protein kinase c-lamda/iota) (apkc-lambda/iota). [swissprot;acc:p41743] 6374.65 7145.59 1.12094
    SUMO3 Squared ubiquitin-like protein smt3a. [swissprot;acc:p55854] 23948 28164.1 1.17605
    665 ARHGEF3 Rooted rho guanine nucleotide exchange factor 3; rhogef protein; 59.8 kda protein; exchange factor found in platelets and leukemic and neuronal tissues, xpln. [refseq;acc:nm_019555] 51.6042 55.574 1.07693
    HEY2 Ranked hairy/enhancer-of-split related with yrpw motif 2; gridlock; hes-related repressor protein 1. [refseq;acc:nm_012259] 229.072 216.576 1.0577
    LSM6 Squared u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8] 18960.3 22298 1.17604
    NUMB Measured numb protein homolog (h-numb) (protein s171). [swissprot;acc:p49757] 6374.65 7145.59 1.12094
    666 HES1 Ranked transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [swissprot;acc:q14469] 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
    - 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/