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 Network Comparison Type Value Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 1962 to 2011 of 66312 in total
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Network Comparison Type
    		Value Type
    		Interaction Map
    		red
    		network_comparison
    		green
    123 PLK1 serine/threonine-protein kinase plk (ec 2.7.1.-) (plk-1) (serine- threonine protein kinase 13) (stpk13). [swissprot;acc:p53350] Subtracted Rooted Low confidence 68.1979 5.385 73.5829
    PPP1R2 protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] Divided Squared High confidence 192904 1.52896 126167
    RRAGB ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] Subtracted Low confidence 56860.4 7826.1 64686.5
    SNRPD1 small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Ranked High confidence 227.032 33.976 193.056
    STRN striatin. [swissprot;acc:o43815] Low confidence 214.085 13.289 200.796
    TIA1 nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] Divided Rooted High confidence 54.6527 1.24375 67.9743
    TMED10 transmembrane protein tmp21 precursor (21 kda transmembrane trafficking protein) (p24delta) (s31iii125) (s31i125) (tmp-21-i). [swissprot;acc:p49755] Subtracted Measured Low confidence 11403 849.1 12252.1
    124 AQP4 aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [swissprot;acc:p55087] Squared High confidence 71389.9 24647.7 96037.6
    BCL6 b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [swissprot;acc:p41182] Divided Low confidence 81993.8 1.14016 71914
    CTSZ cathepsin z precursor (ec 3.4.22.-) (cathepsin x) (cathepsin p). [swissprot;acc:q9ubr2] Subtracted Rooted 68.1979 5.385 73.5829
    DAZAP1 daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] Ranked 220.268 13.271 206.997
    FAM89B mouse mammary turmor virus receptor homolog 1. [refseq;acc:nm_152832] Divided Rooted 63.5737 1.07715 68.4785
    FOSL1 fos-related antigen 1 (fra-1). [swissprot;acc:p15407] Subtracted Measured High confidence 4944.3 2093.74 7038.04
    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] Divided Ranked 208.52 1.21519 171.595
    MAGEA8 melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] Measured Low confidence 11285.3 1.0937 10318.5
    MAP1LC3B microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] High confidence 24255.7 1.33501 18168.9
    NFYA ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511] Subtracted Rooted 46.7419 14.1918 60.9337
    PIGB phosphatidylinositol glycan, class b. [refseq;acc:nm_004855] Measured Low confidence 11403 849.1 12252.1
    PPP1R2P9 type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] Divided Squared High confidence 192779 1.52884 126095
    PSEN2 presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Subtracted Ranked 285.684 33.45 252.234
    RRAGA ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] Squared Low confidence 56706.1 7711.9 64418
    SLC11A2 natural resistance-associated macrophage protein 2 (nramp 2) (divalent metal transporter 1) (dmt1). [swissprot;acc:p49281] Divided Ranked 224.763 1.06742 210.566
    TIAL1 nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] Rooted High confidence 54.6625 1.24304 67.9477
    125 AQP5 aquaporin 5. [swissprot;acc:p55064] Subtracted Squared 71388.5 24646.7 96035.2
    B9D1 b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] Divided Ranked Low confidence 213.243 1.0674 227.616
    CPSF2 cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] Subtracted Squared 59004.9 7558 51446.9
    CTBP2 c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545] Divided 81761.4 1.13985 71730.2
    HMG20A high-mobility group 20a. [refseq;acc:nm_018200] Ranked High confidence 208.588 1.21429 171.778
    MAGEC1 melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] Measured Low confidence 11285.3 1.0937 10318.5
    MAP1LC3A microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] High confidence 24255.7 1.33501 18168.9
    NFU1 hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] Subtracted 12471.7 2090 14561.7
    PROM1 prominin-like protein 1 precursor (antigen ac133) (cd133 antigen). [swissprot;acc:o43490] Ranked Low confidence 220.268 13.271 206.997
    RRS1 ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050] Divided Squared High confidence 189976 1.52616 124480
    SENP8 sentrin-specific protease 8 (ec 3.4.22.-) (sentrin/sumo-specific protease senp8) (cysteine protease fksg8). [swissprot;acc:q96ld8] Subtracted Rooted Low confidence 67.0736 5.3742 72.4478
    SEPT2 septin 2 (nedd5 protein homolog). [swissprot;acc:q15019] Measured 10168.5 828.2 10996.7
    SKP1A s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991] Ranked High confidence 285.684 33.45 252.234
    SNRPD1 small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Divided Rooted 54.8203 1.23921 67.934
    SON son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583] Subtracted 35.6294 14.1825 49.8119
    SPAG7 sperm associated antigen 7. [refseq;acc:nm_004890] Divided Low confidence 132.137 1.0766 122.736
    126 ADIPOR2 adiponectin receptor 2. [refseq;acc:nm_024551] 66.1599 1.07613 71.1967
    AQP2 aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181] Subtracted Squared High confidence 71387.4 24646 96033.4
    ARHGEF5 rho guanine nucleotide exchange factor 5 (guanine nucleotide regulatory protein tim) (oncogene tim) (p60 tim) (transforming immortalized mammary oncogene). [swissprot;acc:q12774] Divided Low confidence 58231.9 1.13919 51117.1
    ATG4B cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Measured High confidence 24250 1.33499 18164.9
    FBXW7 f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315] Subtracted Ranked 285.684 33.45 252.234
    HMG20A high-mobility group 20a. [refseq;acc:nm_018200] Rooted 60.9353 14.1587 75.094
    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] Divided 60.9342 1.23311 75.1387
    LASS2 lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Ranked Low confidence 191.688 1.06707 179.639
    Subtracted Measured 7098.44 786.54 7884.98
    MAGEA4 melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] Divided 11285.3 1.0937 10318.5
    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] Subtracted Ranked 226.892 13.231 213.661

    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/