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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 208 to 257 of 8289 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Interaction Map
    		red
    		green
    		network_comparison
    104 HOMER2 homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] High confidence 252.371 202.016 1.24926
    105 E2F1 transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [swissprot;acc:q01094] Low confidence 220.497 205.364 1.07369
    GNB1 guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901] High confidence 266.716 333.165 1.24914
    106 COQ7 ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] 252.329 202.004 1.24913
    E2F2 transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] Low confidence 220.497 205.364 1.07369
    107 FAM89B mouse mammary turmor virus receptor homolog 1. [refseq;acc:nm_152832] 227.429 211.97 1.07293
    HOMER1 homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] High confidence 252.309 201.998 1.24907
    108 DLGAP3 disks large-associated protein 3 (dap-3) (sap90/psd-95-associated protein 3) (sapap3) (psd-95/sap90 binding protein 3) (fragment). [swissprot;acc:o95886] Low confidence 197.731 212.069 1.07251
    HOMER3 homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] High confidence 252.296 201.995 1.24902
    109 GNB4 guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0] 266.933 333.281 1.24856
    NEURL neuralized-like. [refseq;acc:nm_004210] Low confidence 232.704 216.996 1.07239
    110 no value disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6] 197.752 212.031 1.07221
    DTX2 deltex 2. [refseq;acc:nm_020892] High confidence 333.144 267.393 1.2459
    111 DTX1 deltex homolog 1; hdx-1. [refseq;acc:nm_004416] 332.925 267.274 1.24563
    VPS33A vacuolar protein sorting 33a (hvps33a). [swissprot;acc:q96ax1] Low confidence 203.914 190.189 1.07217
    112 CREG1 cellular repressor of e1a-stimulated genes. [refseq;acc:nm_003851] 197.762 212.013 1.07206
    PBK 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] High confidence 332.874 267.246 1.24557
    113 CREG2 cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836] Low confidence 197.763 212.011 1.07205
    KHDRBS3 kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] High confidence 332.874 267.246 1.24557
    114 DLGAP1 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] Low confidence 197.779 211.983 1.07182
    KHDRBS1 kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] High confidence 332.874 267.246 1.24557
    115 DLGAP4 disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [swissprot;acc:q9y2h0] Low confidence 197.779 211.983 1.07182
    KHDRBS2 kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] High confidence 332.874 267.246 1.24557
    116 GNB3 guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520] 268.565 334.483 1.24545
    VPS18 vacuolar protein sorting 18 (hvps18). [swissprot;acc:q9p253] Low confidence 204.161 190.791 1.07008
    117 F13A1 coagulation factor xiii a chain precursor (ec 2.3.2.13) (protein- glutamine gamma-glutamyltransferase a chain) (transglutaminase a chain). [swissprot;acc:p00488] 226.395 211.713 1.06935
    NEURL neuralized-like. [refseq;acc:nm_004210] High confidence 332.326 266.948 1.24491
    118 NDUFA12 nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09] 284.753 228.934 1.24382
    TGM1 protein-glutamine gamma-glutamyltransferase k (ec 2.3.2.13) (transglutaminase k) (tgase k) (tgk) (tg(k)) (transglutaminase 1) (epidermal tgase). [swissprot;acc:p22735] Low confidence 226.395 211.713 1.06935
    119 NDUFS4 nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181] High confidence 318.982 259.004 1.23157
    SLC11A1 natural resistance-associated macrophage protein 1 (nramp 1). [swissprot;acc:p49279] Low confidence 225.666 211.107 1.06897
    120 DVL1 segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] 203.016 189.965 1.0687
    KCND2 potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] High confidence 269.278 327.709 1.21699
    121 CTH cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] 269.254 327.655 1.2169
    DVL2 segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] Low confidence 203.007 189.985 1.06854
    122 no value nanos (fragment). [sptrembl;acc:q8wy41] 203.66 217.479 1.06785
    KCND3 potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980] High confidence 269.248 327.642 1.21688
    123 DVL3 segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] Low confidence 202.96 190.094 1.06768
    KCND1 potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] High confidence 269.23 327.601 1.21681
    124 HMG20B high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339] 208.52 171.595 1.21519
    SLC11A2 natural resistance-associated macrophage protein 2 (nramp 2) (divalent metal transporter 1) (dmt1). [swissprot;acc:p49281] Low confidence 224.763 210.566 1.06742
    125 B9D1 b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] 213.243 227.616 1.0674
    HMG20A high-mobility group 20a. [refseq;acc:nm_018200] High confidence 208.588 171.778 1.21429
    126 LASS2 lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Low confidence 191.688 179.639 1.06707
    STAMBPL1 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] High confidence 94 114 1.21277
    127 CHMP2A putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453]
    VPS33B vacuolar protein sorting 33b (hvps33b). [swissprot;acc:q9h267] Low confidence 203.678 190.88 1.06705
    128 STAMBP associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] High confidence 94 114 1.21277
    STRN striatin. [swissprot;acc:o43815] Low confidence 214.085 200.796 1.06618
    129 COL4A3BP goodpasture antigen-binding protein (ec 2.7.1.37) (gpbp) (collagen type iv alpha 3 binding protein) (star-related lipid transfer protein 11) (stard11) (start domain-containing protein 11). [swissprot;acc:q9y5p4] 220.969 235.572 1.06609

    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/