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 7514 to 7563 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		red
    		green
    		network_comparison
    1879 LIMS2 lim and senescent cell antigen-like domains 2; ilk-binding protein. [refseq;acc:nm_017980] Measured 6076.66 6463.12 1.0636
    NUCB2 nucleobindin 2 precursor (dna-binding protein nefa). [swissprot;acc:p80303] Ranked 212.186 214.467 1.01075
    NUDT12 nudix (nucleoside diphosphate linked moiety x)-type motif 12. [refseq;acc:nm_031438] Squared 12933 14159.6 1.09484
    1880 CDA cytidine deaminase (ec 3.5.4.5) (cytidine aminohydrolase). [swissprot;acc:p32320] Ranked 220.852 223.225 1.01074
    COPG coatomer gamma subunit (gamma-coat protein) (gamma-cop). [swissprot;acc:q9y678] Rooted 84.5408 82.1199 1.02948
    DRD4 d(4) dopamine receptor (d(2c) dopamine receptor). [swissprot;acc:p21917] Measured 6076.66 6463.12 1.0636
    SERPINB12 serpin b12. [swissprot;acc:q96p63] Squared 26276.4 28767.6 1.09481
    1881 no value dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03] Ranked 210.592 208.355 1.01074
    keratin associated protein 9-4; keratin associated protein 9.4. [refseq;acc:nm_033191] Measured 6076.68 6462.56 1.0635
    COPZ1 coatomer zeta-1 subunit (zeta-1 coat protein) (zeta-1 cop) (cgi-120) (hspc181). [swissprot;acc:q9y3c3] Rooted 84.5408 82.1199 1.02948
    SERPINB7 megsin (tp55) (serpin b7). [swissprot;acc:o75635] Squared 26276.4 28767.6 1.09481
    1882 no value hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]
    ARCN1 coatomer delta subunit (delta-coat protein) (delta-cop) (archain). [swissprot;acc:p48444] Rooted 84.5408 82.1199 1.02948
    EIF2S3 eukaryotic translation initiation factor 2 subunit 3 (eukaryotic translation initiation factor 2 gamma subunit) (eif-2-gamma). [swissprot;acc:p41091] Measured 5490.24 5838.67 1.06346
    RPL28 60s ribosomal protein l28. [swissprot;acc:p46779] Ranked 215.896 213.61 1.0107
    1883 NR1H2 oxysterols receptor lxr-beta (liver x receptor beta) (nuclear orphan receptor lxr-beta) (ubiquitously-expressed nuclear receptor) (nuclear receptor ner). [swissprot;acc:p55055] Squared 26276.4 28767.6 1.09481
    PFKP 6-phosphofructokinase, type c (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme c) (pfk-c) (6-phosphofructokinase, platelet type). [swissprot;acc:q01813] Ranked 240.317 242.881 1.01067
    PPIE peptidyl-prolyl cis-trans isomerase e (ec 5.2.1.8) (ppiase e) (rotamase e) (cyclophilin e) (cyclophilin 33). [swissprot;acc:q9unp9] Rooted 84.5408 82.1199 1.02948
    PSMD1 26s proteasome non-atpase regulatory subunit 1 (26s proteasome regulatory subunit s1) (26s proteasome subunit p112). [swissprot;acc:q99460] Measured 5826 6195.48 1.06342
    1884 ADRM1 adhesion regulating molecule 1 precursor (110 kda cell membrane glycoprotein) (gp110). [swissprot;acc:q16186]
    C16orf70 upf0183 protein. [swissprot;acc:q9bsu1] Squared 26276.4 28767.6 1.09481
    COPZ2 coatomer zeta-2 subunit (zeta-2 coat protein) (zeta-2 cop). [swissprot;acc:q9p299] Rooted 84.5408 82.1199 1.02948
    OLA1 putative gtp-binding protein ptd004 (pro2455). [swissprot;acc:q9ntk5] Ranked 215.081 217.373 1.01066
    1885 no value ischemia/reperfusion inducible protein. [refseq;acc:nm_024640] Rooted 61.8736 63.6965 1.02946
    ARG1 arginase 1 (ec 3.5.3.1) (liver-type arginase). [swissprot;acc:p05089] Ranked 204.44 206.615 1.01064
    SERPINC1 antithrombin-iii precursor (atiii) (pro0309). [swissprot;acc:p01008] Squared 26276.4 28767.6 1.09481
    UCHL5 ubiquitin carboxyl-terminal hydrolase isozyme l5 (ec 3.4.19.12) (uch- l5) (ubiquitin thiolesterase l5) (ubiquitin c-terminal hydrolase uch37) (cgi-70) (ad-019). [swissprot;acc:q9y5k5] Measured 5826 6195.48 1.06342
    1886 ARG2 arginase ii, mitochondrial precursor (ec 3.5.3.1) (non-hepatic arginase) (kidney-type arginase). [swissprot;acc:p78540] Ranked 204.512 206.682 1.01061
    C19orf2 rna polymerase ii subunit 5-mediating protein (rpb5-mediating protein). [swissprot;acc:o94763] Measured 5826 6195.48 1.06342
    EIF2B1 translation initiation factor eif-2b alpha subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q14232] Squared 26276.4 28767.6 1.09481
    PCAF p300/cbp-associated factor (ec 2.3.1.-) (p/caf) (histone acetylase pcaf). [swissprot;acc:q92831] Rooted 69.8124 71.8658 1.02941
    1887 no value protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [refseq;acc:nm_003981] Measured 5438.6 5783.11 1.06335
    GCN5L2 general control of amino acid synthesis protein 5-like 2 (ec 2.3.1.-) (histone acetyltransferase gcn5) (hsgcn5). [swissprot;acc:q92830] Rooted 69.8109 71.8643 1.02941
    SARM1 sterile alpha and tir motif containing 1; sterile alpha and heat/armadillo motif protein, ortholog of drosophila. [refseq;acc:nm_015077] Ranked 220.896 218.577 1.01061
    SERPINB4 squamous cell carcinoma antigen 1 (scca-1) (protein t4-a). [swissprot;acc:p29508] Squared 26276.4 28767.6 1.09481
    1888 BRD4 bromodomain-containing protein 4 (hunk1 protein). [swissprot;acc:o60885] Measured 5438.6 5783.11 1.06335
    ICT1 immature colon carcinoma transcript 1 (digestion substraction 1) (ds- 1). [swissprot;acc:q14197] Ranked 218.414 216.131 1.01056
    MAPK8IP3 c-jun-amino-terminal kinase interacting protein 3 (jnk-interacting protein 3) (jip-3) (jnk map kinase scaffold protein 3) (mitogen- activated protein kinase 8-interacting protein 3). [swissprot;acc:q9upt6] Rooted 62.2848 64.1142 1.02937
    NR1H3 oxysterols receptor lxr-alpha (liver x receptor alpha) (nuclear orphan receptor lxr-alpha). [swissprot;acc:q13133] Squared 26276.4 28767.6 1.09481
    1889 BRDT testis-specific bromodomain protein. [refseq;acc:nm_001726] Measured 5438.68 5783.2 1.06335
    DHPS deoxyhypusine synthase (ec 2.5.1.46) (dhs). [swissprot;acc:p49366] Rooted 64.3493 66.2289 1.02921
    RAB3IL1 rab3a interacting protein (rabin3)-like 1. [refseq;acc:nm_013401] Ranked 211.27 209.067 1.01054
    RPL30 60s ribosomal protein l30. [swissprot;acc:p04645] Squared 12981.1 14211.2 1.09476
    1890 CYB5R2 cytochrome b5 reductase b5r.2. [refseq;acc:nm_016229] Rooted 65.3912 67.3008 1.0292
    LRRC4 nag14 protein. [refseq;acc:nm_022143] Measured 5438.6 5783.11 1.06335
    MRPL36 60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6] Squared 12685.5 13884.4 1.09451
    RAB3IP rab3a interacting protein isoform alpha 1; rabin3; ssx2 interacting protein. [refseq;acc:nm_022456] Ranked 211.314 209.111 1.01054
    1891 BRD3 bromodomain-containing protein 3 (ring3-like protein). [swissprot;acc:q15059] Measured 5438.18 5782.62 1.06334
    CYB5R1 cytochrome b5 reductase 1 (b5r.1). [refseq;acc:nm_016243] Rooted 65.3912 67.3008 1.0292
    DAZAP1 daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] Squared 24776.1 27116.5 1.09446

    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/