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 1200 to 1249 of 6456 in total
    Value Type  : Measured
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    description
    Network Comparison Type
    red
    green
    network_comparison
    600 histone h2b.e (h2b/e). [swissprot;acc:q99879] Divided 3946.32 4475.47 1.13409
    601 hepatoma-derived growth factor (hdgf) (high-mobility group protein 1- like 2) (hmg-1l2). [swissprot;acc:p51858] Subtracted 4533.74 5279.4 745.66
    symplekin. [swissprot;acc:q92797] Divided 15213.4 13418.1 1.1338
    602 ataxin 2 related protein isoform a; ataxin-2 domain protein. [refseq;acc:nm_007245] 4864.66 5514.87 1.13366
    pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [refseq;acc:nm_138574] Subtracted 4533.74 5279.4 745.66
    603 ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] Divided 4864.66 5514.87 1.13366
    probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [swissprot;acc:p26196] Subtracted 4533.74 5279.4 745.66
    604 rw1 protein (fragment). [swissprot;acc:q92545]
    vinculin (metavinculin). [swissprot;acc:p18206] Divided 5958.23 6743.37 1.13177
    605 probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] 6143.52 6950.75 1.1314
    rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908] Subtracted 6079.26 6824.47 745.21
    606 calcium-transporting atpase type 2c, member 1 (ec 3.6.3.8) (atpase 2c1) (atp-dependent ca(2+) pump pmr1) (hussy-28). [swissprot;acc:p98194] Divided 6148.94 6955.76 1.13121
    t-complex associated-testis-expressed 1-like (protein 91/23). [swissprot;acc:p51808] Subtracted 10231.8 9487.34 744.46
    607 double-strand break repair protein mre11a (mre11 homolog 1). [swissprot;acc:p49959]
    likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235] Divided 14976.4 13246.6 1.13058
    608 forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] Subtracted 2234.68 2978.53 743.85
    nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [swissprot;acc:p25208] Divided 4510.61 5098.74 1.13039
    609 b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] 3886.62 3438.82 1.13022
    forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] Subtracted 2234.73 2978.57 743.84
    610 forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] 2236.61 2980.35 743.74
    kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] Divided 8430.03 9518.11 1.12907
    611 dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [swissprot;acc:q13409] 5148.71 5811.74 1.12878
    fibulin-2 precursor. [swissprot;acc:p98095] Subtracted 8670.59 9412.9 742.31
    612 cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520] 5480.24 6222.04 741.8
    eukaryotic translation initiation factor 3 subunit 2 (eif-3 beta) (eif3 p36) (eif3i) (tgf-beta receptor interacting protein 1) (trip-1). [swissprot;acc:q13347] Divided 3975.77 4485.05 1.1281
    613 transforming protein rhoc (h9). [swissprot;acc:p08134] Subtracted 5480.24 6222.04 741.8
    trinucleotide repeat containing 15. [refseq;acc:nm_015575] Divided 3975.77 4485.05 1.1281
    614 solute carrier family 4 (anion exchanger), member 1, adaptor protein; kidney anion exchanger adaptor protein; kanadaptin; lung cancer oncogene 3. [refseq;acc:nm_018158] 11222.2 9948.93 1.12798
    thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762] Subtracted 5480.24 6222.04 741.8
    615 3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325]
    cyclin-dependent kinases regulatory subunit 2 (cks-2). [swissprot;acc:p33552] Divided 11222.2 9948.93 1.12798
    616 catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [refseq;acc:nm_003798]
    transforming protein rhoa (h12). [swissprot;acc:p06749] Subtracted 5480.24 6222.04 741.8
    617 dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [swissprot;acc:o14576] Divided 5162.52 5822.47 1.12783
    splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] Subtracted 4532.73 5269.33 736.6
    618 dna mismatch repair protein mlh3 (mutl protein homolog 3). [swissprot;acc:q9uhc1] 6327.86 7064.13 736.27
    nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [swissprot;acc:q13232] Divided 7878.27 8879.08 1.12703
    619 nucleolar protein nop56 (nucleolar protein 5a). [swissprot;acc:o00567] 3879.99 4371.24 1.12661
    ornithine decarboxylase (ec 4.1.1.17) (odc). [swissprot;acc:p11926] Subtracted 6811.2 7547.35 736.15
    620 aminoadipate-semialdehyde synthase; lysine-ketoglutarate reductase /saccharopine dehydrogenase; lysine-2-oxoglutarate reductase; aminoadipic semialdehyde synthase. [refseq;acc:nm_005763] 6807.78 7543.28 735.5
    ferritin heavy chain (ferritin h subunit). [swissprot;acc:p02794] Divided 6227.87 7012.9 1.12605
    621 ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [refseq;acc:nm_017647] 4115.39 4633.96 1.12601
    ornithine decarboxylase-like protein (ec 4.1.1.17) (odc-paralogue) (odc-p). [swissprot;acc:q96a70] Subtracted 6805.86 7540.99 735.13
    622 mitochondrial ferritin; ferritin heavy chain-like; ferritin h subunit. [refseq;acc:nm_177478] Divided 6228.42 7013.21 1.126
    ornithine decarboxylase antizyme inhibitor. [swissprot;acc:o14977] Subtracted 6805.45 7540.5 735.05
    623 cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836] Divided 6228.39 7013.19 1.126
    eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730] Subtracted 4490.28 5222.25 731.97
    624 bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933]
    dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6] Divided 6228.39 7013.19 1.126
    625 disks large-associated protein 1 (dap-1) (guanylate kinase-associated protein) (hgkap) (sap90/psd-95-associated protein 1) (sapap1) (psd- 95/sap90 binding protein 1). [swissprot;acc:o14490]

    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/