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