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 1962 to 2011 of 66312 in total
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		Network Comparison Type
    		Interaction Map
    		red
    		green
    		network_comparison
    123 PLK1 serine/threonine-protein kinase plk (ec 2.7.1.-) (plk-1) (serine- threonine protein kinase 13) (stpk13). [swissprot;acc:p53350] Rooted Subtracted Low confidence 68.1979 73.5829 5.385
    PPP1R2 protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] Squared Divided High confidence 192904 126167 1.52896
    RRAGB ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] Subtracted Low confidence 56860.4 64686.5 7826.1
    SNRPD1 small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Ranked High confidence 227.032 193.056 33.976
    STRN striatin. [swissprot;acc:o43815] Low confidence 214.085 200.796 13.289
    TIA1 nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] Rooted Divided High confidence 54.6527 67.9743 1.24375
    TMED10 transmembrane protein tmp21 precursor (21 kda transmembrane trafficking protein) (p24delta) (s31iii125) (s31i125) (tmp-21-i). [swissprot;acc:p49755] Measured Subtracted Low confidence 11403 12252.1 849.1
    124 AQP4 aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [swissprot;acc:p55087] Squared High confidence 71389.9 96037.6 24647.7
    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 71914 1.14016
    CTSZ cathepsin z precursor (ec 3.4.22.-) (cathepsin x) (cathepsin p). [swissprot;acc:q9ubr2] Rooted Subtracted 68.1979 73.5829 5.385
    DAZAP1 daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] Ranked 220.268 206.997 13.271
    FAM89B mouse mammary turmor virus receptor homolog 1. [refseq;acc:nm_152832] Rooted Divided 63.5737 68.4785 1.07715
    FOSL1 fos-related antigen 1 (fra-1). [swissprot;acc:p15407] Measured Subtracted High confidence 4944.3 7038.04 2093.74
    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] Ranked Divided 208.52 171.595 1.21519
    MAGEA8 melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] Measured Low confidence 11285.3 10318.5 1.0937
    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 18168.9 1.33501
    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] Rooted Subtracted 46.7419 60.9337 14.1918
    PIGB phosphatidylinositol glycan, class b. [refseq;acc:nm_004855] Measured Low confidence 11403 12252.1 849.1
    PPP1R2P9 type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] Squared Divided High confidence 192779 126095 1.52884
    PSEN2 presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Ranked Subtracted 285.684 252.234 33.45
    RRAGA ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] Squared Low confidence 56706.1 64418 7711.9
    SLC11A2 natural resistance-associated macrophage protein 2 (nramp 2) (divalent metal transporter 1) (dmt1). [swissprot;acc:p49281] Ranked Divided 224.763 210.566 1.06742
    TIAL1 nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] Rooted High confidence 54.6625 67.9477 1.24304
    125 AQP5 aquaporin 5. [swissprot;acc:p55064] Squared Subtracted 71388.5 96035.2 24646.7
    B9D1 b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] Ranked Divided Low confidence 213.243 227.616 1.0674
    CPSF2 cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] Squared Subtracted 59004.9 51446.9 7558
    CTBP2 c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545] Divided 81761.4 71730.2 1.13985
    HMG20A high-mobility group 20a. [refseq;acc:nm_018200] Ranked High confidence 208.588 171.778 1.21429
    MAGEC1 melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] Measured Low confidence 11285.3 10318.5 1.0937
    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 18168.9 1.33501
    NFU1 hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] Subtracted 12471.7 14561.7 2090
    PROM1 prominin-like protein 1 precursor (antigen ac133) (cd133 antigen). [swissprot;acc:o43490] Ranked Low confidence 220.268 206.997 13.271
    RRS1 ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050] Squared Divided High confidence 189976 124480 1.52616
    SENP8 sentrin-specific protease 8 (ec 3.4.22.-) (sentrin/sumo-specific protease senp8) (cysteine protease fksg8). [swissprot;acc:q96ld8] Rooted Subtracted Low confidence 67.0736 72.4478 5.3742
    SEPT2 septin 2 (nedd5 protein homolog). [swissprot;acc:q15019] Measured 10168.5 10996.7 828.2
    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 285.684 252.234 33.45
    SNRPD1 small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Rooted Divided 54.8203 67.934 1.23921
    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 49.8119 14.1825
    SPAG7 sperm associated antigen 7. [refseq;acc:nm_004890] Divided Low confidence 132.137 122.736 1.0766
    126 ADIPOR2 adiponectin receptor 2. [refseq;acc:nm_024551] 66.1599 71.1967 1.07613
    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] Squared Subtracted High confidence 71387.4 96033.4 24646
    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 51117.1 1.13919
    ATG4B cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Measured High confidence 24250 18164.9 1.33499
    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] Ranked Subtracted 285.684 252.234 33.45
    HMG20A high-mobility group 20a. [refseq;acc:nm_018200] Rooted 60.9353 75.094 14.1587
    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 75.1387 1.23311
    LASS2 lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Measured Subtracted Low confidence 7098.44 7884.98 786.54
    Ranked Divided 191.688 179.639 1.06707
    MAGEA4 melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] Measured 11285.3 10318.5 1.0937
    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] Ranked Subtracted 226.892 213.661 13.231

    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/