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 Network Comparison Type description Value Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 7164 to 7213 of 16578 in total
    Value Type  : Ranked
    Filtered  : 1
    Rank
    		Hugo
    		Network Comparison Type
    		description
    		Interaction Map
    		red
    		network_comparison
    		green
    1791 VPS72 Subtracted yl-1 protein (transcription factor-like 1). [swissprot;acc:q15906] Low confidence 201.916 3.961 197.955
    1792 ACTN4 alpha-actinin 4 (non-muscle alpha-actinin 4) (f-actin cross linking protein). [swissprot;acc:o43707] High confidence 217.008 2.526 214.482
    AQP5 Divided aquaporin 5. [swissprot;acc:p55064] Low confidence 195.447 1.02014 191.588
    CHKA Subtracted choline kinase (ec 2.7.1.32) (ck) (chetk-alpha). [swissprot;acc:p35790] 199.201 3.961 195.24
    ELAVL4 Divided elav-like protein 4 (paraneoplastic encephalomyelitis antigen hud) (hu-antigen d). [swissprot;acc:p26378] High confidence 217.766 1.01193 215.199
    1793 MAPK8IP3 Subtracted 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] Low confidence 204.532 3.96 208.492
    NME2P1 Divided putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361] High confidence 193.1 1.01193 190.823
    PABPC3 polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361] Low confidence 204.337 1.02014 200.302
    SPTLC1 Subtracted serine palmitoyltransferase 1 (ec 2.3.1.50) (long chain base biosynthesis protein 1) (lcb 1) (serine-palmitoyl-coa transferase 1) (spt 1) (spt1). [swissprot;acc:o15269] High confidence 207.757 2.517 210.274
    1794 no value Divided nucleoside diphosphate kinase b (ec 2.7.4.6) (ndk b) (ndp kinase b) (nm23-h2) (c-myc purine-binding transcription factor puf). [swissprot;acc:p22392] 193.138 1.01193 190.861
    CCNC Subtracted cyclin c. [swissprot;acc:p24863] 217.071 2.507 214.564
    NAPSA napsin 1 precursor (ec 3.4.23.-) (napsin a) (napa) (ta01/ta02) (aspartyl protease 4) (asp 4) (asp4). [swissprot;acc:o96009] Low confidence 198.283 3.96 194.323
    TATDN1 Divided cda11 protein. [refseq;acc:nm_032026] 199.338 1.02014 195.403
    1795 ALDH1L1 Subtracted 10-formyltetrahydrofolate dehydrogenase (ec 1.5.1.6) (10-fthfdh). [swissprot;acc:o75891] 203.414 3.959 199.455
    ELAVL2 Divided elav-like protein 2 (hu-antigen b) (hub) (elav-like neuronal protein 1) (nervous system-specific rna binding protein hel-n1). [swissprot;acc:q12926] High confidence 217.724 1.01193 215.158
    GALNT2 Subtracted polypeptide n-acetylgalactosaminyltransferase 2; udp-galnac transferase 2. [refseq;acc:nm_004481] 216.854 2.504 214.35
    MIP Divided lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [swissprot;acc:p30301] Low confidence 195.447 1.02014 191.589
    1796 GALNTL1 Subtracted similar to expressed sequence ai415388 (fragment). [sptrembl;acc:q8n428] High confidence 216.854 2.504 214.35
    NAPSB aspartyl protease 3 (fragment). [sptrembl;acc:q9uhb3] Low confidence 198.281 3.959 194.322
    TOP2B Divided dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880] High confidence 203.759 1.01193 201.357
    TSNAX translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598] Low confidence 202.745 1.02014 198.743
    1797 DEK Subtracted dek protein. [swissprot;acc:p35659] 203.415 3.959 199.456
    NME2 Divided nucleoside diphosphate kinase a (ec 2.7.4.6) (ndk a) (ndp kinase a) (tumor metastatic process-associated protein) (metastasis inhibition factor nm23) (nm23-h1). [swissprot;acc:p15531] High confidence 193.111 1.01193 190.834
    PQBP1 polyglutamine binding protein 1; nuclear protein containing ww domain 38 kd. [refseq;acc:nm_005710] Low confidence 202.745 1.02014 198.743
    RBM38 Subtracted rna-binding region containing protein 1 (hsrnaseb) (ssdna binding protein seb4) (cll-associated antigen kw-5). [swissprot;acc:q9h0z9] High confidence 218.36 2.486 215.874
    1798 no value myosin vi. [swissprot;acc:q9um54] Low confidence 203.415 3.959 199.456
    EIF2S2 eukaryotic translation initiation factor 2 subunit 2 (eukaryotic translation initiation factor 2 beta subunit) (eif-2-beta). [swissprot;acc:p20042] High confidence 221.525 2.476 224.001
    ELAVL1 Divided elav-like protein 1 (hu-antigen r) (hur). [swissprot;acc:q15717] 217.807 1.01192 215.242
    PSMD8 26s proteasome non-atpase regulatory subunit 8 (26s proteasome regulatory subunit s14) (p31). [swissprot;acc:p48556] Low confidence 200.037 1.02014 196.088
    1799 no value Subtracted helicase (fragment). [sptrembl;acc:q92771] High confidence 187.204 2.475 189.679
    ACTN2 Divided alpha-actinin 2 (alpha actinin skeletal muscle isoform 2) (f-actin cross linking protein). [swissprot;acc:p35609] 217.016 1.01182 214.481
    AQP6 Subtracted aquaporin 6 (aquaporin-2 like) (hkid). [swissprot;acc:q13520] Low confidence 195.243 3.959 191.284
    RDH8 Divided retinol dehydrogenase 8 (all-trans); photoreceptor outer segment all-trans retinol dehydrogenase. [refseq;acc:nm_015725] 199.606 1.02014 195.666
    1800 DDX12 Subtracted dead/h (asp-glu-ala-asp/his) box polypeptide 11; dead/h box-11 (chl1-related helicase gene-1); yeast chl1 homolog. [refseq;acc:nm_030655] High confidence 187.205 2.474 189.679
    DYRK1A Divided dual-specificity tyrosine-phosphorylation regulated kinase 1a (ec 2.7.1.-) (protein kinase minibrain homolog) (mnbh) (hp86) (dual specificity yak1-related kinase). [swissprot;acc:q13627] 217.011 1.0118 214.481
    MLLT4 af-6 protein. [swissprot;acc:p55196] Low confidence 203.545 1.02013 199.529
    TRMT11 Subtracted mds024 protein. [refseq;acc:nm_021820] 202.243 3.959 198.284
    1801 no value Divided dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0] 196.761 1.02013 192.879
    CUGBP1 cug triplet repeat rna-binding protein 1 (cug-bp1) (rna-binding protein brunol-2) (deadenylation factor cug-bp) (50 kda nuclear polyadenylated rna-binding protein) (eden-bp). [swissprot;acc:q92879] High confidence 217.984 1.0118 215.441
    KHK Subtracted ketohexokinase (ec 2.7.1.3) (hepatic fructokinase). [swissprot;acc:p50053] 218.984 2.462 221.446
    REN renin precursor, renal (ec 3.4.23.15) (angiotensinogenase). [swissprot;acc:p00797] Low confidence 198.278 3.958 194.32
    1802 no value purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491] High confidence 218.984 2.462 221.446
    ELP4 Divided elongation protein 4 homolog; pax6 neighbor gene; chromosome 11 open reading frame 19. [refseq;acc:nm_019040] 217.011 1.0118 214.481
    EPN1 Subtracted epsin 1; eh domain-binding mitotic phosphoprotein. [refseq;acc:nm_013333] Low confidence 191.484 3.955 187.529
    HSD17B1 Divided estradiol 17 beta-dehydrogenase 1 (ec 1.1.1.62) (17-beta-hsd 1) (placental 17-beta-hydroxysteroid dehydrogenase) (20 alpha- hydroxysteroid dehydrogenase) (20-alpha-hsd) (e2dh). [swissprot;acc:p14061] 199.594 1.02012 195.657
    1803 no value 17 beta-hydroxysteroid dehydrogenase. [sptrembl;acc:q13034] 199.592 195.655
    DYRK1B dual-specificity tyrosine-phosphorylation regulated kinase 1b (ec 2.7.1.-) (mirk protein kinase). [swissprot;acc:q9y463] High confidence 217.011 1.0118 214.481
    PBX1 Subtracted pre-b-cell leukemia transcription factor-1 (homeobox protein pbx1) (homeobox protein prl). [swissprot;acc:p40424] 206.332 2.458 203.874
    UBE2D2 ubiquitin-conjugating enzyme e2-17 kda 2 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2(17)kb 2). [swissprot;acc:p51669] Low confidence 203.016 3.954 199.062
    1804 no value germ cell-less. [refseq;acc:nm_022471] High confidence 206.335 2.458 203.877

    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/