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 description Gene Hugo Network Comparison Type Value Type red Interaction Map Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 1758 to 1807 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Value Type
    		red
    		green
    		network_comparison
    440 dna topoisomerase ii, alpha isozyme (ec 5.99.1.3). [swissprot;acc:p11388] no value Squared 26348.4 31925.8 1.21168
    docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496] DOK2 Rooted 63.2134 69.352 1.09711
    highly expressed in cancer, rich in leucine heptad repeats. [refseq;acc:nm_006101] NDC80 Ranked 231.802 249.983 1.07843
    441 dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880] TOP2B Squared 26348.7 31924.3 1.21161
    docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704] DOK1 Rooted 63.2134 69.352 1.09711
    grancalcin. [swissprot;acc:p28676] GCA Measured 6251.96 7192.13 1.15038
    grb2-related adaptor protein. [swissprot;acc:q13588] GRAP Ranked 223.457 207.222 1.07835
    442 centromere protein j; centrosomal p4.1-associated protein; lyst-interacting protein lip1; lag-3-associated protein. [refseq;acc:nm_018451] CENPJ Squared 51286.6 42334.5 1.21146
    e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140] ANKS1B Ranked 223.802 207.55 1.0783
    sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] SRI Measured 6251.99 7192.17 1.15038
    tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685] FRK Rooted 63.2134 69.352 1.09711
    443 60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025] no value 50.1766 45.7369 1.09707
    brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732] ARID1B Measured 6252.27 7192.51 1.15038
    neuron navigator 2 isoform l; retinoic acid inducible in neuroblastoma; pore membrane and/or filament interacting like protein 2; helicase helad1. [refseq;acc:nm_145117] NAV2 Ranked 223.79 207.539 1.0783
    translation initiation factor if-2, mitochondrial precursor (if-2mt) (if-2(mt)). [swissprot;acc:p46199] MTIF2 Squared 26472.8 32067.7 1.21135
    444 60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] no value Rooted 50.1636 45.7275 1.09701
    neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443] NAV1 Ranked 223.801 207.549 1.0783
    probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848] EBNA1BP2 Measured 3758.67 4322.87 1.15011
    ubiquitin-conjugating enzyme e2 e1 (ec 6.3.2.19) (ubiquitin-protein ligase e1) (ubiquitin carrier protein e1) (ubch6). [swissprot;acc:p51965] UBE2E1 Squared 58831 48584.2 1.21091
    445 ad24 protein. [refseq;acc:nm_022451] NOC3L Measured 3753.71 4315.95 1.14978
    neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903] NAV3 Ranked 223.801 207.549 1.0783
    ribosomal protein l10-like protein. [refseq;acc:nm_080746] RPL10L Rooted 50.1635 45.7274 1.09701
    ubiquitin-conjugating enzyme e2e 3; ubiquitin carrier protein; ubiquitin-protein ligase. [refseq;acc:nm_006357] UBE2E4P Squared 58831 48584.2 1.21091
    446 eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730] EIF4E Rooted 54.9019 60.2111 1.0967
    growth factor receptor-bound protein 2 (grb2 adapter protein) (sh2/sh3 adapter grb2) (ash protein). [swissprot;acc:p29354] GRB2 Ranked 224.049 207.785 1.07827
    nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366] GNL3 Measured 3766.03 4329.37 1.14958
    ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385] SORBS1 Squared 29335.6 35515.5 1.21066
    447 bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933] BAIAP3 Rooted 54.9019 60.2111 1.0967
    pescadillo homolog 1. [swissprot;acc:o00541] PES1 Measured 3751.14 4310.89 1.14922
    serine/threonine-protein kinase nek2 (ec 2.7.1.37) (nima-related protein kinase 2) (nima-like protein kinase 1) (hspk 21). [swissprot;acc:p51955] NEK2 Ranked 224.049 207.785 1.07827
    sipl protein. [refseq;acc:nm_018269] ADI1 Squared 30155.1 36495 1.21024
    448 calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] CAPN1 20350.3 16816.1 1.21017
    microtubule-actin crosslinking factor 1, isoform 4. [swissprot;acc:q96pk2] MACF1 Ranked 228.468 246.338 1.07822
    ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385] SORBS1 Measured 6259.3 7190.91 1.14884
    protein transport protein sec61 gamma subunit. [swissprot;acc:p38384] SEC61G Rooted 50.1671 45.7563 1.0964
    449 bullous pemphigoid antigen 1 isoforms 1/2/3/4/5/8 (230 kda bullous pemphigoid antigen) (bpa) (hemidesmosomal plaque protein) (dystonia musculorum protein) (fragment). [swissprot;acc:q03001] DST Ranked 228.463 246.33 1.07821
    calpain 2, large [catalytic] subunit precursor (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (m-type) (m-calpain) (millimolar-calpain) (calpain large polypeptide l2). [swissprot;acc:p17655] CAPN2 Squared 20348.5 16817.2 1.20998
    dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [swissprot;acc:p30876] POLR2B Rooted 50.162 45.7659 1.09606
    wd-repeat protein 12 (ytm1 homolog). [swissprot;acc:q9gzl7] WDR12 Measured 3761.59 4319.69 1.14837
    450 acetyl-coa carboxylase 2 (ec 6.4.1.2) (acc-beta) [includes: biotin carboxylase (ec 6.3.4.14)]. [swissprot;acc:o00763] ACACB Squared 31646.1 38288.7 1.2099
    l-myc-1 proto-oncogene protein. [swissprot;acc:p12524] MYCL1 Measured 4889.21 5610.52 1.14753
    signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] SRP9 Ranked 235.94 218.837 1.07815
    ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085] CMPK Rooted 50.4595 46.0411 1.09597
    451 mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061] MRPL17 50.268 45.8663
    n-myc proto-oncogene protein. [swissprot;acc:p04198] MYCN Measured 4889.71 5610.69 1.14745
    polymerase (rna) iii (dna directed) (62kd). [refseq;acc:nm_006468] POLR3C Ranked 239.092 257.705 1.07785
    small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] no value Squared 17543.3 21222.5 1.20972
    452 adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] Rooted 50.4595 46.0415 1.09596
    ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] Ranked 224.161 207.972 1.07784
    small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] SNRPF Squared 17543.3 21222.5 1.20972

    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/