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 Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1501 to 1550 of 6456 in total
    Value Type  : Ranked
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Network Comparison Type
    		red
    		green
    		network_comparison
    751 dnaj homolog subfamily b member 5 (heat shock protein hsp40-3) (heat shock protein cognate 40) (hsc40) (hsp40-2). [swissprot;acc:o75953] DNAJB5 Subtracted 210.946 221.225 10.279
    u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695] no value Divided 223.463 212.875 1.04974
    752 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] DNAJB1 Subtracted 210.946 221.225 10.279
    step ii splicing factor slu7. [refseq;acc:nm_006425] SLU7 Divided 223.463 212.875 1.04974
    753 eukaryotic peptide chain release factor subunit 1 (erf1) (eukaryotic release factor 1) (tb3-1) (c11 protein). [swissprot;acc:p46055] ETF1 Subtracted 210.946 221.225 10.279
    lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428] LBP Divided 224.434 235.583 1.04968
    754 microsomal signal peptidase 25 kda subunit (ec 3.4.-.-) (spase 25 kda subunit) (spc25). [swissprot;acc:q15005] SPCS2
    suppressor of actin mutations 2-like isoform b; dj1033b10.5. [refseq;acc:nm_022553] VPS52 Subtracted 210.946 221.225 10.279
    755 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] no value 224.244 234.511 10.267
    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 Divided 224.434 235.583 1.04968
    756 40s ribosomal protein s21. [swissprot;acc:p35265] RPS21 Subtracted 224.244 234.511 10.267
    cleft lip and palate associated transmembrane protein 1. [refseq;acc:nm_001294] CLPTM1 Divided 224.434 235.583 1.04968
    757 bactericidal permeability-increasing protein precursor (bpi) (cap 57). [swissprot;acc:p17213] BPI
    cytoplasmic antiproteinase 3 (cap3) (cap-3) (protease inhibitor 9) (serpin b9). [swissprot;acc:p50453] SERPINB9 Subtracted 224.244 234.511 10.267
    758 maspin precursor (protease inhibitor 5). [swissprot;acc:p36952] no value
    phospholipid transfer protein precursor (lipid transfer protein ii). [swissprot;acc:p55058] PLTP Divided 224.434 235.583 1.04968
    759 bomapin (protease inhibitor 10) (serpin b10). [swissprot;acc:p48595] SERPINB10 Subtracted 224.244 234.511 10.267
    osteoclast stimulating factor 1. [swissprot;acc:q92882] OSTF1 Divided 231.809 243.289 1.04952
    760 plasminogen activator inhibitor-2 precursor (pai-2) (placental plasminogen activator inhibitor) (monocyte arg-serpin) (urokinase inhibitor). [swissprot;acc:p05120] SERPINB8 Subtracted 224.244 234.511 10.267
    upf0202 protein kiaa1709. [swissprot;acc:q9h0a0] NAT10 Divided 246.055 234.458 1.04946
    761 serpin b11. [swissprot;acc:q96p15] no value Subtracted 224.244 234.511 10.267
    signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191] CBLB Divided 213.325 203.303 1.0493
    762 cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681] CBL 213.256 203.237
    placental thrombin inhibitor (cytoplasmic antiproteinase) (cap) (protease inhibitor 6) (pi-6). [swissprot;acc:p35237] SERPINB6 Subtracted 224.244 234.511 10.267
    763 cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452] no value
    putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [swissprot;acc:q9y5n5] N6AMT1 Divided 228.78 218.091 1.04901
    764 leukocyte elastase inhibitor (lei) (monocyte/neutrophil elastase inhibitor) (m/nei) (ei). [swissprot;acc:p30740] SERPINB1 Subtracted 224.244 234.511 10.267
    u4/u6-associated rna splicing factor. [refseq;acc:nm_004698] PRPF3 Divided 222.082 211.707 1.04901
    765 eukaryotic translation initiation factor 3 subunit 9 (eif-3 eta) (eif3 p116) (eif3 p110) (eif3b). [swissprot;acc:p55884] EIF3B Subtracted 243.067 232.805 10.262
    hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [swissprot;acc:q9y5r4] HEMK1 Divided 229.045 218.343 1.04901
    766 protein tara (trio-associated repeat on actin) (hrihfb2122). [swissprot;acc:q9h2d6] TRIOBP 213.804 224.226 1.04875
    sorting nexin 6 (traf4-associated factor 2). [swissprot;acc:q9unh7] SNX6 Subtracted 209.191 219.332 10.141
    767 dna-directed rna polymerase ii 14.5 kda polypeptide (ec 2.7.7.6) (rpb9) (rpb14.5). [swissprot;acc:p36954] POLR2I 228.563 238.668 10.105
    rho interacting protein 3. [refseq;acc:nm_015134] no value Divided 213.803 224.224 1.04874
    768 dnaj homolog subfamily b member 4 (heat shock 40 kda protein 1 homolog) (heat shock protein 40 homolog) (hsp40 homolog). [swissprot;acc:q9udy4] DNAJB4 210.946 221.225 1.04873
    signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191] CBLB Subtracted 213.325 203.303 10.022
    769 cab2. [refseq;acc:nm_033419] PERLD1 Divided 210.946 221.225 1.04873
    cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681] CBL Subtracted 213.256 203.237 10.019
    770 dnaj homolog subfamily b member 5 (heat shock protein hsp40-3) (heat shock protein cognate 40) (hsc40) (hsp40-2). [swissprot;acc:o75953] DNAJB5 Divided 210.946 221.225 1.04873
    ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] RRAGA Subtracted 59 49 10
    771 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] DNAJB1 Divided 210.946 221.225 1.04873
    ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] RRAGC Subtracted 59 49 10
    772 eukaryotic peptide chain release factor subunit 1 (erf1) (eukaryotic release factor 1) (tb3-1) (c11 protein). [swissprot;acc:p46055] ETF1 Divided 210.946 221.225 1.04873
    ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] RRAGB Subtracted 59 49 10
    773 anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] ANLN
    suppressor of actin mutations 2-like isoform b; dj1033b10.5. [refseq;acc:nm_022553] VPS52 Divided 210.946 221.225 1.04873
    774 mitochondrial 28s ribosomal protein s2 (mrp-s2) (cgi-91). [swissprot;acc:q9y399] MRPS2 Subtracted 221.716 231.501 9.785
    multiple coagulation factor deficiency 2; neural stem cell derived neuronal survival protein; multiple coagulation factor deficiency protein 2. [refseq;acc:nm_139279] MCFD2 Divided 225.996 215.535 1.04854
    775 histone deacetylase 2 (hd2). [swissprot;acc:q92769] no value 226.003 215.541
    u3 snornp protein 4 homolog. [refseq;acc:nm_033416] IMP4 Subtracted 221.676 231.453 9.777

    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/