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 Network Comparison Type description 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
    		Hugo
    		Value Type
    		Network Comparison Type
    		description
    		red
    		green
    		network_comparison
    332 NEUROD6 Ranked Divided neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] 312 284 1.09859
    NUBP1 Squared nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] 14464.3 18142.8 1.25432
    PLRG1 Measured pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] 5051.16 5975.51 1.183
    SCYE1 Rooted Subtracted multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904] 59.0951 66.4332 7.3381
    SHROOM3 Divided shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859] 60.6732 67.2827 1.10894
    VAV2 Measured Subtracted vav-2 protein. [swissprot;acc:p52735] 6660.02 7697.78 1037.76
    333 no value Ranked transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] 265.634 244.304 21.33
    ACADVL Rooted acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] 95.4476 102.785 7.3374
    DTX2 Measured deltex 2. [refseq;acc:nm_020892] 1618.84 2651.88 1033.04
    GTPBP4 Rooted Divided nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4] 49.0526 54.3781 1.10857
    MYH13 Squared Subtracted myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] 19321 12542.6 6778.4
    NEUROD1 Ranked Divided neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] 312 284 1.09859
    NUBP2 Squared nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] 14464.3 18142.8 1.25432
    PRPF19 Measured nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502] 5039.63 5961.83 1.18299
    334 CANT1 Squared ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793] 64975.9 81151.2 1.24894
    DTX1 Measured Subtracted deltex homolog 1; hdx-1. [refseq;acc:nm_004416] 1629.21 2662.12 1032.91
    ENOPH1 Squared e-1 enzyme. [refseq;acc:nm_021204] 30903.8 37638.1 6734.3
    NEUROD4 Ranked Divided neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] 312 284 1.09859
    PLRG1 Rooted pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] 58.6096 64.9655 1.10844
    RRM2B Ranked Subtracted ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] 232.473 211.207 21.266
    SEPT4 Measured Divided 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] 14924.4 17655.2 1.18298
    TFIP11 Rooted Subtracted tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] 58.2964 65.5926 7.2962
    335 C15orf15 Squared Divided ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [refseq;acc:nm_016304] 30651.3 38253.3 1.24802
    CHD5 Ranked chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] 312 284 1.09859
    DDX56 Measured probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] 3494.31 4129.6 1.18181
    PBK Subtracted 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] 1631.67 2664.55 1032.88
    RBBP7 Rooted histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] 52.7146 60.0088 7.2942
    RPL24 Squared 60s ribosomal protein l24 (l30). [swissprot;acc:p38663] 30924.3 37652.3 6728
    RPS11 Rooted Divided 40s ribosomal protein s11. [swissprot;acc:p04643] 50.4705 45.5342 1.10841
    SCYE1 Ranked Subtracted multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904] 223.273 202.423 20.85
    336 ASAH1 Squared acid ceramidase precursor (ec 3.5.1.23) (acylsphingosine deacylase) (n-acylsphingosine amidohydrolase) (ac) (putative 32 kda heart protein) (php32). [swissprot;acc:q13510] 36109.8 42811.6 6701.8
    CDK2AP1 Ranked Divided 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] 312 284 1.09859
    KHDRBS3 Measured Subtracted kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] 1631.67 2664.55 1032.88
    POLE4 Divided dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] 3751.3 4431.34 1.18128
    POLI Rooted Subtracted polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] 59.4073 66.7002 7.2929
    POLR1E Ranked rna polymerase i associated factor 53. [refseq;acc:nm_022490] 241.045 261.874 20.829
    RBPJ Squared Divided j kappa-recombination signal binding protein (rbp-j kappa). [swissprot;acc:q06330] 46785.7 58383.2 1.24789
    RPL11 Rooted 60s ribosomal protein l11. [swissprot;acc:p39026] 50.3167 45.4063 1.10814
    337 no value Measured homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 20446.1 24136.4 1.18049
    Ranked 60s ribosomal protein l12. [swissprot;acc:p30050] 243.583 267.527 1.0983
    Squared Subtracted nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] 28895.6 35572.8 6677.2
    CPA6 Rooted Divided carboxypeptidase b precursor. [refseq;acc:nm_020361] 77.5801 70.0182 1.108
    HIVEP3 Squared human immunodeficiency virus type i enhancer binding protein 3. [refseq;acc:nm_024503] 46785.7 58383.2 1.24789
    KHDRBS1 Measured Subtracted kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] 1631.67 2664.55 1032.88
    PXN Rooted paxillin. [swissprot;acc:p49023] 59.4073 66.7002 7.2929
    STT3B Ranked source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] 200.691 179.88 20.811
    338 no value Divided 60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] 243.583 267.528 1.0983
    CPA3 Rooted mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] 77.58 70.0181 1.108
    HIVEP1 Squared zinc finger protein 40 (human immunodeficiency virus type i enhancer- binding protein 1) (hiv-ep1) (major histocompatibility complex binding protein 1) (mbp-1) (positive regulatory domain ii binding factor 1) (prdii-bf1). [swissprot;acc:p15822] 46785.7 58383.2 1.24789
    HOXB4 Measured homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] 20446.1 24136.4 1.18049

    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/