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 2858 to 2907 of 16578 in total
    Value Type  : Ranked
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Network Comparison Type
    		Interaction Map
    		red
    		green
    		network_comparison
    715 GARS glycyl-trna synthetase (ec 6.1.1.14) (glycine--trna ligase) (glyrs). [swissprot;acc:p41250] Divided Low confidence 203.107 197.646 1.02763
    POLE dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864] Subtracted 204.279 198.814 5.465
    UMPS uridine 5'-monophosphate synthase (ump synthase) [includes: orotate phosphoribosyltransferase (ec 2.4.2.10) (oprtase); orotidine 5'- phosphate decarboxylase (ec 4.1.1.23) (ompdecase)]. [swissprot;acc:p11172] High confidence 224.434 235.583 11.149
    716 no value repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273] Low confidence 199.669 194.204 5.465
    CLPTM1 cleft lip and palate associated transmembrane protein 1. [refseq;acc:nm_001294] High confidence 224.434 235.583 11.149
    CPZ cpz gene product. [refseq;acc:nm_003652] Divided 223.121 211.685 1.05402
    EEF1D elongation factor 1-delta (ef-1-delta) (antigen ny-co-4). [swissprot;acc:p29692] Low confidence 203.552 198.081 1.02762
    717 BPI bactericidal permeability-increasing protein precursor (bpi) (cap 57). [swissprot;acc:p17213] Subtracted High confidence 224.434 235.583 11.149
    BTF3 transcription factor btf3 (rna polymerase b transcription factor 3). [swissprot;acc:p20290] Divided Low confidence 204.133 198.652 1.02759
    CPE carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870] High confidence 223.121 211.685 1.05402
    EPS8L1 epidermal growth factor receptor pathway substrate 8-like protein 1 isoform c; epidermal growth factor receptor pathway substrate 8-related protein 1; eps8-related protein 1. [refseq;acc:nm_139204] Subtracted Low confidence 206.474 201.013 5.461
    718 ARPC1B arp2/3 complex 41 kda subunit (p41-arc) (actin-related protein 2/3 complex subunit 1b). [swissprot;acc:o15143] Divided 201.612 196.213 1.02752
    CPXM1 potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [swissprot;acc:q96sm3] High confidence 223.121 211.685 1.05402
    GARS glycyl-trna synthetase (ec 6.1.1.14) (glycine--trna ligase) (glyrs). [swissprot;acc:p41250] Subtracted Low confidence 203.107 197.646 5.461
    PLTP phospholipid transfer protein precursor (lipid transfer protein ii). [swissprot;acc:p55058] High confidence 224.434 235.583 11.149
    719 APEX2 apurinic/apyrimidinic endonuclease 2; apurinic/apyrimidinic endonuclease-like 2; apex nuclease-like 2. [refseq;acc:nm_014481] Low confidence 202.569 197.109 5.46
    DCTD deoxycytidylate deaminase (ec 3.5.4.12) (dcmp deaminase). [swissprot;acc:p32321] High confidence 230.516 241.641 11.125
    NOL5A nucleolar protein nop56 (nucleolar protein 5a). [swissprot;acc:o00567] Divided 247.769 235.074 1.054
    STUB1 stip1 homology and u-box containing protein 1; serologically defined colon cancer antigen 7; carboxy terminus of hsp70p-interacting protein; heat shock protein a binding protein 2 (c-terminal). [refseq;acc:nm_005861] Low confidence 199.172 193.841 1.0275
    720 EPS8 epidermal growth factor receptor kinase substrate eps8. [swissprot;acc:q12929] Subtracted 206.469 201.011 5.458
    POLE dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864] Divided 204.279 198.814 1.02749
    RPLP2 60s acidic ribosomal protein p2. [swissprot;acc:p05387] High confidence 231.92 244.435 1.05396
    TREH trehalase precursor (ec 3.2.1.28) (alpha,alpha-trehalase) (alpha,alpha-trehalose glucohydrolase). [swissprot;acc:o43280] Subtracted 217.952 206.902 11.05
    721 ASCC2 asc-1 complex subunit p100. [refseq;acc:nm_032204] Low confidence 211.636 206.184 5.452
    EXOC5 exocyst complex component sec10 (hsec10). [swissprot;acc:o00471] Divided High confidence 214.765 203.8 1.0538
    Subtracted 10.965
    SNX16 sorting nexin 16. [swissprot;acc:p57768] Divided Low confidence 203.411 197.971 1.02748
    722 IGF2BP1 igf-ii mrna-binding protein 1. [refseq;acc:nm_006546] 205.571 200.075 1.02747
    NET1 neuroepithelial cell transforming gene 1; guanine nucleotide regulatory protein (oncogene); rho guanine nucleotide exchange factor (gef) 8. [refseq;acc:nm_005863] Subtracted High confidence 244.447 233.508 10.939
    TREH trehalase precursor (ec 3.2.1.28) (alpha,alpha-trehalase) (alpha,alpha-trehalose glucohydrolase). [swissprot;acc:o43280] Divided 217.952 206.902 1.05341
    YEATS4 glioma-amplified sequence-41; numa binding protein 1. [refseq;acc:nm_006530] Subtracted Low confidence 198.424 192.974 5.45
    723 no value histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351] Divided High confidence 244.842 232.577 1.05274
    ARHGEF3 rho guanine nucleotide exchange factor 3; rhogef protein; 59.8 kda protein; exchange factor found in platelets and leukemic and neuronal tissues, xpln. [refseq;acc:nm_019555] Subtracted 244.447 233.508 10.939
    PARN poly(a)-specific ribonuclease (deadenylation nuclease); deadenylation nuclease. [refseq;acc:nm_002582] Divided Low confidence 203.779 198.331 1.02747
    RNASEH1 ribonuclease h1 (ec 3.1.26.4) (rnase h1) (ribonuclease h type ii). [swissprot;acc:o60930] Subtracted 206.457 201.008 5.449
    724 no value dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9] Divided High confidence 244.842 232.577 1.05274
    ACY1 aminoacylase-1 (ec 3.5.1.14) (n-acyl-l-amino-acid amidohydrolase) (acy-1). [swissprot;acc:q03154] Low confidence 201.765 196.371 1.02747
    PARN poly(a)-specific ribonuclease (deadenylation nuclease); deadenylation nuclease. [refseq;acc:nm_002582] Subtracted 203.779 198.331 5.448
    UTP20 down-regulated in metastasis. [refseq;acc:nm_014503] High confidence 244.447 233.508 10.939
    725 ACO1 iron-responsive element binding protein 1 (ire-bp 1) (iron regulatory protein 1) (irp1) (ferritin repressor protein) (aconitate hydratase) (ec 4.2.1.3) (citrate hydro-lyase) (aconitase). [swissprot;acc:p21399] Low confidence 200.577 195.136 5.441
    IGF2BP3 igf-ii mrna-binding protein 3; kh domain containing protein overexpressed in cancer. [refseq;acc:nm_006547] Divided 205.563 200.075 1.02743
    MVK mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426] High confidence 235.296 247.673 1.0526
    SLC35B1 solute carrier family 35, member b1; udp-galactose transporter related. [refseq;acc:nm_005827] Subtracted 214.679 225.568 10.889
    726 DDX39 dead (asp-glu-ala-asp) box polypeptide 39 isoform 1; nuclear rna helicase, decd variant of dead box family. [refseq;acc:nm_005804] Divided Low confidence 192.552 187.412 1.02743
    FTSJ3 ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [refseq;acc:nm_017647] High confidence 244.495 232.419 1.05196
    SNX16 sorting nexin 16. [swissprot;acc:p57768] Subtracted Low confidence 203.411 197.971 5.44
    XAB2 xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7] High confidence 222.825 211.966 10.859
    727 ARPC1A actin-related protein 2/3 complex subunit 1a (sop2-like protein). [swissprot;acc:q92747] Divided Low confidence 201.571 196.189 1.02743
    EPS8L2 epidermal growth factor receptor pathway substrate 8-like protein 2; eps8-related protein 2; epidermal growth factor receptor pathway substrate 8-related protein 2. [refseq;acc:nm_022772] Subtracted 206.435 201.001 5.434
    NUAK1 probable serine/threonine-protein kinase kiaa0537 (ec 2.7.1.-). [swissprot;acc:o60285] Divided High confidence 208.873 219.71 1.05188

    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/