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 Network Comparison Type Hugo Value Type description Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 1975 to 2024 of 66312 in total
    Filtered  : 1
    Rank
    		Network Comparison Type
    		Hugo
    		Value Type
    		description
    		Interaction Map
    		red
    		network_comparison
    		green
    124 Divided SLC11A2 Ranked natural resistance-associated macrophage protein 2 (nramp 2) (divalent metal transporter 1) (dmt1). [swissprot;acc:p49281] Low confidence 224.763 1.06742 210.566
    TIAL1 Rooted nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] High confidence 54.6625 1.24304 67.9477
    Subtracted AQP4 Squared aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [swissprot;acc:p55087] 71389.9 24647.7 96037.6
    CTSZ Rooted cathepsin z precursor (ec 3.4.22.-) (cathepsin x) (cathepsin p). [swissprot;acc:q9ubr2] Low confidence 68.1979 5.385 73.5829
    DAZAP1 Ranked daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] 220.268 13.271 206.997
    FOSL1 Measured fos-related antigen 1 (fra-1). [swissprot;acc:p15407] High confidence 4944.3 2093.74 7038.04
    NFYA Rooted 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] 46.7419 14.1918 60.9337
    PIGB Measured phosphatidylinositol glycan, class b. [refseq;acc:nm_004855] Low confidence 11403 849.1 12252.1
    PSEN2 Ranked presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] High confidence 285.684 33.45 252.234
    RRAGA Squared ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] Low confidence 56706.1 7711.9 64418
    125 Divided B9D1 Ranked b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] 213.243 1.0674 227.616
    CTBP2 Squared c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545] 81761.4 1.13985 71730.2
    HMG20A Ranked high-mobility group 20a. [refseq;acc:nm_018200] High confidence 208.588 1.21429 171.778
    MAGEC1 Measured melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] 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
    RRS1 Squared ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050] 189976 1.52616 124480
    SNRPD1 Rooted small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] 54.8203 1.23921 67.934
    SPAG7 sperm associated antigen 7. [refseq;acc:nm_004890] Low confidence 132.137 1.0766 122.736
    Subtracted AQP5 Squared aquaporin 5. [swissprot;acc:p55064] High confidence 71388.5 24646.7 96035.2
    CPSF2 cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] Low confidence 59004.9 7558 51446.9
    NFU1 Measured hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] High confidence 12471.7 2090 14561.7
    PROM1 Ranked prominin-like protein 1 precursor (antigen ac133) (cd133 antigen). [swissprot;acc:o43490] Low confidence 220.268 13.271 206.997
    SENP8 Rooted sentrin-specific protease 8 (ec 3.4.22.-) (sentrin/sumo-specific protease senp8) (cysteine protease fksg8). [swissprot;acc:q96ld8] 67.0736 5.3742 72.4478
    SEPT2 Measured septin 2 (nedd5 protein homolog). [swissprot;acc:q15019] 10168.5 828.2 10996.7
    SKP1A Ranked 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] High confidence 285.684 33.45 252.234
    SON Rooted 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] 35.6294 14.1825 49.8119
    126 Divided ADIPOR2 adiponectin receptor 2. [refseq;acc:nm_024551] Low confidence 66.1599 1.07613 71.1967
    ARHGEF5 Squared rho guanine nucleotide exchange factor 5 (guanine nucleotide regulatory protein tim) (oncogene tim) (p60 tim) (transforming immortalized mammary oncogene). [swissprot;acc:q12774] 58231.9 1.13919 51117.1
    ATG4B Measured cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] High confidence 24250 1.33499 18164.9
    HMG20B Rooted 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] 60.9342 1.23311 75.1387
    LASS2 Ranked lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Low confidence 191.688 1.06707 179.639
    MAGEA4 Measured melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] 11285.3 1.0937 10318.5
    PPP1CA Squared serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129] High confidence 189976 1.52616 124480
    STAMBPL1 Ranked associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] 94 1.21277 114
    Subtracted AQP2 Squared 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] 71387.4 24646 96033.4
    FBXW7 Ranked 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] 285.684 33.45 252.234
    HMG20A Rooted high-mobility group 20a. [refseq;acc:nm_018200] 60.9353 14.1587 75.094
    LASS2 Measured lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Low confidence 7098.44 786.54 7884.98
    NDUFS4 Ranked 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] 226.892 13.231 213.661
    NEDD8 Rooted ubiquitin-like protein nedd8. [swissprot;acc:q15843] 67.0736 5.3742 72.4478
    PCF11 Squared pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913] 58331.7 7295.7 51036
    RINT1 Measured rad50-interacting protein 1. [refseq;acc:nm_021930] High confidence 450.5 1944 2394.5
    127 Divided no value melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] Low confidence 11285.3 1.0937 10318.5
    Squared cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] High confidence 88432.6 1.51365 58423.3
    CHMP2A Ranked putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] 94 1.21277 114
    HMG20A Rooted high-mobility group 20a. [refseq;acc:nm_018200] 60.9353 1.23236 75.094
    JUND Measured transcription factor jun-d. [swissprot;acc:p17535] 5638.2 1.33436 7523.39
    SLC16A2 Squared monocarboxylate transporter 8 (mct 8) (x-linked pest-containing transporter) (mct 7). [swissprot;acc:p36021] Low confidence 63904 1.13908 72791.6
    VPS33B Ranked vacuolar protein sorting 33b (hvps33b). [swissprot;acc:q9h267] 203.678 1.06705 190.88
    VPS41 Rooted vacuolar assembly protein vps41 homolog (s53). [swissprot;acc:p49754] 70.0842 1.07532 75.3627

    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/