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 [...,...].
    description Rank Gene Hugo Value Type Network Comparison Type Interaction Map red Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 873 to 922 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    description
    		Rank
    		Hugo
    		red
    		green
    		network_comparison
    down-regulated in metastasis. [refseq;acc:nm_014503] 787 UTP20 244.447 233.508 1.04685
    dpy-30-like protein. [swissprot;acc:q9c005] 1815 no value 220.462 217.926 1.01164
    dr1-associated protein 1; negative cofactor 2 alpha; dr1-associated corepressor. [refseq;acc:nm_006442] 1468 DRAP1 212.001 207.937 1.01954
    dual specificity mitogen-activated protein kinase kinase 1 (ec 2.7.1.-) (map kinase kinase 1) (mapkk 1) (erk activator kinase 1) (mapk/erk kinase 1) (mek1). [swissprot;acc:q02750] 2069 MAP2K1 217.555 215.807 1.0081
    dual specificity mitogen-activated protein kinase kinase 2 (ec 2.7.1.-) (map kinase kinase 2) (mapkk 2) (erk activator kinase 2) (mapk/erk kinase 2) (mek2). [swissprot;acc:p36507] 2072 MAP2K2
    dual specificity mitogen-activated protein kinase kinase 3 (ec 2.7.1.-) (map kinase kinase 3) (mapkk 3) (mapk/erk kinase 3). [swissprot;acc:p46734] 2385 MAP2K3 210.595 209.767 1.00395
    dual specificity mitogen-activated protein kinase kinase 4 (ec 2.7.1.-) (map kinase kinase 4) (jnk activating kinase 1) (c-jun n- terminal kinase kinase 1) (jnkk) (sapk/erk kinase 1) (sek1). [swissprot;acc:p45985] 2326 MAP2K4 220.076 219.05 1.00468
    dual specificity mitogen-activated protein kinase kinase 6 (ec 2.7.1.-) (map kinase kinase 6) (mapkk 6) (mapk/erk kinase 6) (sapkk3). [swissprot;acc:p52564] 2384 MAP2K6 210.57 209.737 1.00397
    dual specificity mitogen-activated protein kinase kinase 7 (ec 2.7.1.-) (map kinase kinase 7) (mapkk 7) (mapk/erk kinase 7) (jnk activating kinase 2) (c-jun n-terminal kinase kinase 2) (jnk kinase 2) (jnkk 2). [swissprot;acc:o14733] 2139 MAP2K7 221.248 222.788 1.00696
    dual specificity protein phosphatase 11 (ec 3.1.3.48) (rna/rnp complex-intereracting phosphatase) (phosphatase that interacts with rna/rnp complex 1). [swissprot;acc:o75319] 2926 DUSP11 0.00001 0.00001 1
    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] 1800 DYRK1A 217.011 214.481 1.0118
    dual-specificity tyrosine-phosphorylation regulated kinase 1b (ec 2.7.1.-) (mirk protein kinase). [swissprot;acc:q9y463] 1803 DYRK1B
    dymeclin. [refseq;acc:nm_017653] 2055 DYM 218.79 216.981 1.00834
    dynactin 4. [refseq;acc:nm_032486] 426 DCTN5 233.142 252.253 1.08197
    dynactin complex 50 kda subunit (50 kda dynein-associated polypeptide) (dynamitin) (dctn-50) (dynactin 2). [swissprot;acc:q13561] 1549 DCTN2 225.159 221.424 1.01687
    dynamin 1-like protein isoform 3; dynamin-like protein. [refseq;acc:nm_005690] 2081 DNM1L 215.967 214.28 1.00787
    dynein 2 light intermediate chain. [refseq;acc:nm_016008] 2962 DYNC2LI1 0.00001 0.00001 1
    dynein intermediate chain 1, axonemal (axonemal dynein intermediate chain 1). [swissprot;acc:q9ui46] 3029 DNAI1
    dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [swissprot;acc:o14576] 1005 DYNC1I1 225.448 218.232 1.03307
    dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [swissprot;acc:q13409] 998 DYNC1I2 225.557 218.271 1.03338
    dynein light chain 2. [refseq;acc:nm_080677] 647 DYNLL2 216.731 229.549 1.05914
    dyskerin (nucleolar protein nap57) (cbf5 homolog). [swissprot;acc:o60832] 1085 DKC1 231.007 237.864 1.02968
    dystrobrevin alpha (dystrobrevin-alpha). [swissprot;acc:q9y4j8] 2583 DTNA 213.415 213.743 1.00154
    dystrobrevin beta (beta-dystrobrevin) (dtn-b). [swissprot;acc:o60941] 2581 DTNB 213.428 213.756
    dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122] 1599 DTNBP1 217.871 214.404 1.01617
    dystrophin. [swissprot;acc:p11532] 2584 no value 213.422 213.75 1.00154
    e-1 enzyme. [refseq;acc:nm_021204] 2251 ENOPH1 208.315 207.061 1.00606
    e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409] 1984 EP400 219.26 217.193 1.00952
    e1b-55kda-associated protein 5 isoform a. [refseq;acc:nm_007040] 484 HNRPUL1 237.109 254.667 1.07405
    e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140] 442 ANKS1B 223.802 207.55 1.0783
    eap30 subunit of ell complex. [refseq;acc:nm_007241] 163 SNF8 209.299 249.187 1.19058
    early endosome antigen 1, 162kd; early endosome-associated protein. [refseq;acc:nm_003566] 1660 EEA1 228.654 231.933 1.01434
    ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] 203 TBC1D10A 201.515 228.752 1.13516
    ecotropic viral integration site 5; neuroblastoma stage 4s gene. [refseq;acc:nm_005665] 1437 EVI5 218.829 214.493 1.02022
    ecotropic virus integration 1 site protein. [swissprot;acc:q03112] 3170 EVI1 0.00001 0.00001 1
    egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215] 200 EGFL7 242.718 276.018 1.1372
    eh-domain containing protein 1 (testilin) (hpast1). [swissprot;acc:q9h4m9] 1455 EHD1 207.024 211.085 1.01962
    eh-domain containing protein 2. [swissprot;acc:q9nzn4] 1457 EHD2 211.086
    eh-domain containing protein 3. [swissprot;acc:q9nzn3] 1458 EHD3
    eh-domain containing protein 4 (eh domain-containing protein fksg7) (hepatocellular carcinoma-associated protein 10/11). [swissprot;acc:q9h223] 1456 EHD4
    eif-5a2 protein. [refseq;acc:nm_020390] 2105 EIF5A2 208.591 210.111 1.00729
    elac homolog 2; putative prostate cancer susceptibility protein; elac (e. coli) homolog 2. [refseq;acc:nm_018127] 1538 ELAC2 228.419 232.376 1.01732
    elav-like protein 1 (hu-antigen r) (hur). [swissprot;acc:q15717] 1798 ELAVL1 217.807 215.242 1.01192
    elav-like protein 2 (hu-antigen b) (hub) (elav-like neuronal protein 1) (nervous system-specific rna binding protein hel-n1). [swissprot;acc:q12926] 1795 ELAVL2 217.724 215.158 1.01193
    elav-like protein 3 (hu-antigen c) (huc) (paraneoplastic cerebellar degeneration-associated antigen) (paraneoplastic limbic encephalitis antigen 21). [swissprot;acc:q14576] 1791 no value 217.866 215.295 1.01194
    elav-like protein 4 (paraneoplastic encephalomyelitis antigen hud) (hu-antigen d). [swissprot;acc:p26378] 1792 ELAVL4 217.766 215.199 1.01193
    electron transfer flavoprotein alpha-subunit, mitochondrial precursor (alpha-etf). [swissprot;acc:p13804] 2441 ETFA 180.137 180.732 1.0033
    electron transfer flavoprotein beta-subunit (beta-etf). [swissprot;acc:p38117] 2353 ETFB 182.232 183.027 1.00436
    electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial precursor (ec 1.5.5.1) (etf-qo) (etf-ubiquinone oxidoreductase) (etf dehydrogenase) (electron-transferring- flavoprotein dehydrogenase). [swissprot;acc:q16134] 2016 ETFDH 199.092 197.301 1.00908
    elks protein. [refseq;acc:nm_015064] 1061 ERC1 218.162 211.648 1.03078

    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/