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 2651 to 2700 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Value Type
    		Network Comparison Type
    		red
    		green
    		network_comparison
    332 multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904] Rooted Subtracted 59.0951 66.4332 7.3381
    neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] Ranked Divided 312 284 1.09859
    nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] Squared 14464.3 18142.8 1.25432
    pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] Measured 5051.16 5975.51 1.183
    shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859] Rooted 60.6732 67.2827 1.10894
    vav-2 protein. [swissprot;acc:p52735] Measured Subtracted 6660.02 7697.78 1037.76
    333 acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] Rooted 95.4476 102.785 7.3374
    deltex 2. [refseq;acc:nm_020892] Measured 1618.84 2651.88 1033.04
    myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] Squared 19321 12542.6 6778.4
    neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] Ranked Divided 312 284 1.09859
    nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502] Measured 5039.63 5961.83 1.18299
    nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4] Rooted 49.0526 54.3781 1.10857
    nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] Squared 14464.3 18142.8 1.25432
    transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] Ranked Subtracted 265.634 244.304 21.33
    334 ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793] Squared Divided 64975.9 81151.2 1.24894
    deltex homolog 1; hdx-1. [refseq;acc:nm_004416] Measured Subtracted 1629.21 2662.12 1032.91
    e-1 enzyme. [refseq;acc:nm_021204] Squared 30903.8 37638.1 6734.3
    neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] Ranked Divided 312 284 1.09859
    pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] Rooted 58.6096 64.9655 1.10844
    ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] Ranked Subtracted 232.473 211.207 21.266
    septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236] Measured Divided 14924.4 17655.2 1.18298
    tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] Rooted Subtracted 58.2964 65.5926 7.2962
    335 40s ribosomal protein s11. [swissprot;acc:p04643] Divided 50.4705 45.5342 1.10841
    60s ribosomal protein l24 (l30). [swissprot;acc:p38663] Squared Subtracted 30924.3 37652.3 6728
    chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] Ranked Divided 312 284 1.09859
    histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] Rooted Subtracted 52.7146 60.0088 7.2942
    multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904] Ranked 223.273 202.423 20.85
    probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] Measured Divided 3494.31 4129.6 1.18181
    ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [refseq;acc:nm_016304] Squared 30651.3 38253.3 1.24802
    t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492] Measured Subtracted 1631.67 2664.55 1032.88
    336 60s ribosomal protein l11. [swissprot;acc:p39026] Rooted Divided 50.3167 45.4063 1.10814
    acid ceramidase precursor (ec 3.5.1.23) (acylsphingosine deacylase) (n-acylsphingosine amidohydrolase) (ac) (putative 32 kda heart protein) (php32). [swissprot;acc:q13510] Squared Subtracted 36109.8 42811.6 6701.8
    cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519] Ranked Divided 312 284 1.09859
    dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] Measured 3751.3 4431.34 1.18128
    j kappa-recombination signal binding protein (rbp-j kappa). [swissprot;acc:q06330] Squared 46785.7 58383.2 1.24789
    kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] Measured Subtracted 1631.67 2664.55 1032.88
    polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] Rooted 59.4073 66.7002 7.2929
    rna polymerase i associated factor 53. [refseq;acc:nm_022490] Ranked 241.045 261.874 20.829
    337 60s ribosomal protein l12. [swissprot;acc:p30050] Divided 243.583 267.527 1.0983
    carboxypeptidase b precursor. [refseq;acc:nm_020361] Rooted 77.5801 70.0182 1.108
    homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Measured 20446.1 24136.4 1.18049
    human immunodeficiency virus type i enhancer binding protein 3. [refseq;acc:nm_024503] Squared 46785.7 58383.2 1.24789
    kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] Measured Subtracted 1631.67 2664.55 1032.88
    nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] Squared 28895.6 35572.8 6677.2
    paxillin. [swissprot;acc:p49023] Rooted 59.4073 66.7002 7.2929
    source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] Ranked 200.691 179.88 20.811
    338 60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] Divided 243.583 267.528 1.0983
    homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] Measured 20446.1 24136.4 1.18049
    importin beta-1 subunit (karyopherin beta-1 subunit) (nuclear factor p97) (importin 90). [swissprot;acc:q14974] Squared Subtracted 28895.6 35572.8 6677.2
    kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] Measured 1631.67 2664.55 1032.88

    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/