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 Hugo Network Comparison Type Value Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 2651 to 2700 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Network Comparison Type
    		Value Type
    		red
    		network_comparison
    		green
    332 multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904] SCYE1 Subtracted Rooted 59.0951 7.3381 66.4332
    neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] NEUROD6 Divided Ranked 312 1.09859 284
    nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] NUBP1 Squared 14464.3 1.25432 18142.8
    pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] PLRG1 Measured 5051.16 1.183 5975.51
    shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859] SHROOM3 Rooted 60.6732 1.10894 67.2827
    vav-2 protein. [swissprot;acc:p52735] VAV2 Subtracted Measured 6660.02 1037.76 7697.78
    333 acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] ACADVL Rooted 95.4476 7.3374 102.785
    deltex 2. [refseq;acc:nm_020892] DTX2 Measured 1618.84 1033.04 2651.88
    myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] MYH13 Squared 19321 6778.4 12542.6
    neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] NEUROD1 Divided Ranked 312 1.09859 284
    nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502] PRPF19 Measured 5039.63 1.18299 5961.83
    nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4] GTPBP4 Rooted 49.0526 1.10857 54.3781
    nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] NUBP2 Squared 14464.3 1.25432 18142.8
    transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] no value Subtracted Ranked 265.634 21.33 244.304
    334 ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793] CANT1 Divided Squared 64975.9 1.24894 81151.2
    deltex homolog 1; hdx-1. [refseq;acc:nm_004416] DTX1 Subtracted Measured 1629.21 1032.91 2662.12
    e-1 enzyme. [refseq;acc:nm_021204] ENOPH1 Squared 30903.8 6734.3 37638.1
    neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] NEUROD4 Divided Ranked 312 1.09859 284
    pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] PLRG1 Rooted 58.6096 1.10844 64.9655
    ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] RRM2B Subtracted Ranked 232.473 21.266 211.207
    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] SEPT4 Divided Measured 14924.4 1.18298 17655.2
    tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] TFIP11 Subtracted Rooted 58.2964 7.2962 65.5926
    335 40s ribosomal protein s11. [swissprot;acc:p04643] RPS11 Divided 50.4705 1.10841 45.5342
    60s ribosomal protein l24 (l30). [swissprot;acc:p38663] RPL24 Subtracted Squared 30924.3 6728 37652.3
    chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] CHD5 Divided Ranked 312 1.09859 284
    histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] RBBP7 Subtracted Rooted 52.7146 7.2942 60.0088
    multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904] SCYE1 Ranked 223.273 20.85 202.423
    probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] DDX56 Divided Measured 3494.31 1.18181 4129.6
    ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [refseq;acc:nm_016304] C15orf15 Squared 30651.3 1.24802 38253.3
    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] PBK Subtracted Measured 1631.67 1032.88 2664.55
    336 60s ribosomal protein l11. [swissprot;acc:p39026] RPL11 Divided Rooted 50.3167 1.10814 45.4063
    acid ceramidase precursor (ec 3.5.1.23) (acylsphingosine deacylase) (n-acylsphingosine amidohydrolase) (ac) (putative 32 kda heart protein) (php32). [swissprot;acc:q13510] ASAH1 Subtracted Squared 36109.8 6701.8 42811.6
    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] CDK2AP1 Divided Ranked 312 1.09859 284
    dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] POLE4 Measured 3751.3 1.18128 4431.34
    j kappa-recombination signal binding protein (rbp-j kappa). [swissprot;acc:q06330] RBPJ Squared 46785.7 1.24789 58383.2
    kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] KHDRBS3 Subtracted Measured 1631.67 1032.88 2664.55
    polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] POLI Rooted 59.4073 7.2929 66.7002
    rna polymerase i associated factor 53. [refseq;acc:nm_022490] POLR1E Ranked 241.045 20.829 261.874
    337 60s ribosomal protein l12. [swissprot;acc:p30050] no value Divided 243.583 1.0983 267.527
    carboxypeptidase b precursor. [refseq;acc:nm_020361] CPA6 Rooted 77.5801 1.108 70.0182
    homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] no value Measured 20446.1 1.18049 24136.4
    human immunodeficiency virus type i enhancer binding protein 3. [refseq;acc:nm_024503] HIVEP3 Squared 46785.7 1.24789 58383.2
    kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] KHDRBS1 Subtracted Measured 1631.67 1032.88 2664.55
    nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] no value Squared 28895.6 6677.2 35572.8
    paxillin. [swissprot;acc:p49023] PXN Rooted 59.4073 7.2929 66.7002
    source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] STT3B Ranked 200.691 20.811 179.88
    338 60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] no value Divided 243.583 1.0983 267.528
    homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] HOXB4 Measured 20446.1 1.18049 24136.4
    importin beta-1 subunit (karyopherin beta-1 subunit) (nuclear factor p97) (importin 90). [swissprot;acc:q14974] KPNB1 Subtracted Squared 28895.6 6677.2 35572.8
    kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] KHDRBS2 Measured 1631.67 1032.88 2664.55

    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/