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 green network_comparison
    Results: HTML CSV LaTeX Showing element 1508 to 1557 of 6456 in total
    Value Type  : Ranked
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Network Comparison Type
    		red
    		green
    		network_comparison
    754 VPS52 suppressor of actin mutations 2-like isoform b; dj1033b10.5. [refseq;acc:nm_022553] Subtracted 210.946 221.225 10.279
    755 no value 40s ribosomal protein sa (p40) (34/67 kda laminin receptor) (colon carcinoma laminin-binding protein) (nem/1chd4) (multidrug resistance- associated protein mgr1-ag). [swissprot;acc:p08865] 224.244 234.511 10.267
    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] Divided 224.434 235.583 1.04968
    756 CLPTM1 cleft lip and palate associated transmembrane protein 1. [refseq;acc:nm_001294]
    RPS21 40s ribosomal protein s21. [swissprot;acc:p35265] Subtracted 224.244 234.511 10.267
    757 BPI bactericidal permeability-increasing protein precursor (bpi) (cap 57). [swissprot;acc:p17213] Divided 224.434 235.583 1.04968
    SERPINB9 cytoplasmic antiproteinase 3 (cap3) (cap-3) (protease inhibitor 9) (serpin b9). [swissprot;acc:p50453] Subtracted 224.244 234.511 10.267
    758 no value maspin precursor (protease inhibitor 5). [swissprot;acc:p36952]
    PLTP phospholipid transfer protein precursor (lipid transfer protein ii). [swissprot;acc:p55058] Divided 224.434 235.583 1.04968
    759 OSTF1 osteoclast stimulating factor 1. [swissprot;acc:q92882] 231.809 243.289 1.04952
    SERPINB10 bomapin (protease inhibitor 10) (serpin b10). [swissprot;acc:p48595] Subtracted 224.244 234.511 10.267
    760 NAT10 upf0202 protein kiaa1709. [swissprot;acc:q9h0a0] Divided 246.055 234.458 1.04946
    SERPINB8 plasminogen activator inhibitor-2 precursor (pai-2) (placental plasminogen activator inhibitor) (monocyte arg-serpin) (urokinase inhibitor). [swissprot;acc:p05120] Subtracted 224.244 234.511 10.267
    761 no value serpin b11. [swissprot;acc:q96p15]
    CBLB signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191] Divided 213.325 203.303 1.0493
    762 CBL cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681] 213.256 203.237
    SERPINB6 placental thrombin inhibitor (cytoplasmic antiproteinase) (cap) (protease inhibitor 6) (pi-6). [swissprot;acc:p35237] Subtracted 224.244 234.511 10.267
    763 no value cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452]
    N6AMT1 putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [swissprot;acc:q9y5n5] Divided 228.78 218.091 1.04901
    764 PRPF3 u4/u6-associated rna splicing factor. [refseq;acc:nm_004698] 222.082 211.707
    SERPINB1 leukocyte elastase inhibitor (lei) (monocyte/neutrophil elastase inhibitor) (m/nei) (ei). [swissprot;acc:p30740] Subtracted 224.244 234.511 10.267
    765 EIF3B eukaryotic translation initiation factor 3 subunit 9 (eif-3 eta) (eif3 p116) (eif3 p110) (eif3b). [swissprot;acc:p55884] 243.067 232.805 10.262
    HEMK1 hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [swissprot;acc:q9y5r4] Divided 229.045 218.343 1.04901
    766 SNX6 sorting nexin 6 (traf4-associated factor 2). [swissprot;acc:q9unh7] Subtracted 209.191 219.332 10.141
    TRIOBP protein tara (trio-associated repeat on actin) (hrihfb2122). [swissprot;acc:q9h2d6] Divided 213.804 224.226 1.04875
    767 no value rho interacting protein 3. [refseq;acc:nm_015134] 213.803 224.224 1.04874
    POLR2I dna-directed rna polymerase ii 14.5 kda polypeptide (ec 2.7.7.6) (rpb9) (rpb14.5). [swissprot;acc:p36954] Subtracted 228.563 238.668 10.105
    768 CBLB signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191] 213.325 203.303 10.022
    DNAJB4 dnaj homolog subfamily b member 4 (heat shock 40 kda protein 1 homolog) (heat shock protein 40 homolog) (hsp40 homolog). [swissprot;acc:q9udy4] Divided 210.946 221.225 1.04873
    769 CBL cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681] Subtracted 213.256 203.237 10.019
    PERLD1 cab2. [refseq;acc:nm_033419] Divided 210.946 221.225 1.04873
    770 DNAJB5 dnaj homolog subfamily b member 5 (heat shock protein hsp40-3) (heat shock protein cognate 40) (hsc40) (hsp40-2). [swissprot;acc:o75953]
    RRAGA ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] Subtracted 59 49 10
    771 DNAJB1 dnaj homolog subfamily b member 1 (heat shock 40 kda protein 1) (heat shock protein 40) (hsp40) (dnaj protein homolog 1) (hdj-1). [swissprot;acc:p25685] Divided 210.946 221.225 1.04873
    RRAGC ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] Subtracted 59 49 10
    772 ETF1 eukaryotic peptide chain release factor subunit 1 (erf1) (eukaryotic release factor 1) (tb3-1) (c11 protein). [swissprot;acc:p46055] Divided 210.946 221.225 1.04873
    RRAGB ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] Subtracted 59 49 10
    773 ANLN anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685]
    VPS52 suppressor of actin mutations 2-like isoform b; dj1033b10.5. [refseq;acc:nm_022553] Divided 210.946 221.225 1.04873
    774 MCFD2 multiple coagulation factor deficiency 2; neural stem cell derived neuronal survival protein; multiple coagulation factor deficiency protein 2. [refseq;acc:nm_139279] 225.996 215.535 1.04854
    MRPS2 mitochondrial 28s ribosomal protein s2 (mrp-s2) (cgi-91). [swissprot;acc:q9y399] Subtracted 221.716 231.501 9.785
    775 no value histone deacetylase 2 (hd2). [swissprot;acc:q92769] Divided 226.003 215.541 1.04854
    IMP4 u3 snornp protein 4 homolog. [refseq;acc:nm_033416] Subtracted 221.676 231.453 9.777
    776 no value dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8] Divided 225.996 215.535 1.04854
    SQSTM1 sequestosome 1; ubiquitin-binding protein p62; phosphotyrosine independent ligand for the lck sh2 domain p62. [refseq;acc:nm_003900] Subtracted 221.965 212.404 9.561
    777 HDAC1 histone deacetylase 1 (hd1). [swissprot;acc:q13547] Divided 225.989 215.53 1.04853
    SCP2 nonspecific lipid-transfer protein, mitochondrial precursor (nsl-tp) (sterol carrier protein 2) (scp-2) (sterol carrier protein x) (scp-x) (scpx). [swissprot;acc:p22307] Subtracted 221.965 212.404 9.561
    778 CTNNB1 beta-catenin (pro2286). [swissprot;acc:p35222] 224.445 214.894 9.551
    SNX6 sorting nexin 6 (traf4-associated factor 2). [swissprot;acc:q9unh7] Divided 209.191 219.332 1.04848
    779 DCTD deoxycytidylate deaminase (ec 3.5.4.12) (dcmp deaminase). [swissprot;acc:p32321] 230.516 241.641 1.04826

    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/