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 Gene Rank Hugo Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2258 to 2307 of 8289 in total
    Network Comparison Type  : Divided
    Value Type  : Ranked
    Filtered  : 1
    description
    		Rank
    		Hugo
    		Interaction Map
    		red
    		green
    		network_comparison
    early endosome antigen 1, 162kd; early endosome-associated protein. [refseq;acc:nm_003566] 1660 EEA1 High confidence 228.654 231.933 1.01434
    2795 Low confidence 201.281 197.852 1.01733
    early growth response protein 1 (egr-1) (krox-24 protein) (zif268) (nerve growth factor-induced protein a) (ngfi-a) (transcription factor etr103) (zinc finger protein 225) (at225). [swissprot;acc:p18146] 3530 EGR1 200.601 197.684 1.01476
    early growth response protein 2 (egr-2) (krox-20 protein) (at591). [swissprot;acc:p11161] 3535 EGR2 200.624 197.712 1.01473
    early growth response protein 3 (egr-3) (zinc finger protein pilot). [swissprot;acc:q06889] 3533 EGR3 200.623 197.711
    early growth response protein 4 (egr-4) (at133). [swissprot;acc:q05215] 3538 EGR4 200.628 197.717 1.01472
    early hematopoietic zinc finger. [refseq;acc:nm_015461] 825 no value 204.914 199.706 1.02608
    ebna-2 co-activator (100kd). [refseq;acc:nm_014390] 2177 201.91 198.138 1.01904
    ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] 203 TBC1D10A High confidence 201.515 228.752 1.13516
    1051 Low confidence 200.439 205.267 1.02409
    ecotropic viral integration site 5; neuroblastoma stage 4s gene. [refseq;acc:nm_005665] 1437 EVI5 High confidence 218.829 214.493 1.02022
    2480 Low confidence 200.094 196.506 1.01826
    ecotropic virus integration 1 site protein. [swissprot;acc:q03112] 1214 EVI1 203.266 198.72 1.02288
    3170 High confidence 0.00001 0.00001 1
    ectonucleoside triphosphate diphosphohydrolase 6 (ec 3.6.1.6) (ntpdase6) (cd39 antigen-like 2). [swissprot;acc:o75354] 1269 no value Low confidence 196.818 192.485 1.02251
    eferin. [swissprot;acc:o75154] 154 RAB11FIP3 183.27 172.702 1.06119
    egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215] 200 EGFL7 High confidence 242.718 276.018 1.1372
    434 Low confidence 214.527 222.034 1.03499
    eh-domain containing protein 1 (testilin) (hpast1). [swissprot;acc:q9h4m9] 1455 EHD1 High confidence 207.024 211.085 1.01962
    3084 Low confidence 198.75 195.519 1.01653
    eh-domain containing protein 2. [swissprot;acc:q9nzn4] 1457 EHD2 High confidence 207.024 211.086 1.01962
    3093 Low confidence 198.752 195.522 1.01652
    eh-domain containing protein 3. [swissprot;acc:q9nzn3] 1458 EHD3 High confidence 207.024 211.086 1.01962
    3089 Low confidence 198.751 195.52 1.01653
    eh-domain containing protein 4 (eh domain-containing protein fksg7) (hepatocellular carcinoma-associated protein 10/11). [swissprot;acc:q9h223] 1456 EHD4 High confidence 207.024 211.086 1.01962
    3086 Low confidence 198.752 195.521 1.01653
    eif-5a2 protein. [refseq;acc:nm_020390] 2105 EIF5A2 High confidence 208.591 210.111 1.00729
    2276 Low confidence 199.76 196.071 1.01881
    elac homolog 2; putative prostate cancer susceptibility protein; elac (e. coli) homolog 2. [refseq;acc:nm_018127] 1538 ELAC2 High confidence 228.419 232.376 1.01732
    3447 Low confidence 196.979 194.031 1.01519
    elav-like protein 1 (hu-antigen r) (hur). [swissprot;acc:q15717] 1489 ELAVL1 202.955 198.692 1.02146
    1798 High confidence 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] 1252 ELAVL2 Low confidence 202.261 197.788 1.02262
    1795 High confidence 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] 1515 no value Low confidence 202.972 198.731 1.02134
    1791 High confidence 217.866 215.295 1.01194
    elav-like protein 4 (paraneoplastic encephalomyelitis antigen hud) (hu-antigen d). [swissprot;acc:p26378] 1474 ELAVL4 Low confidence 202.941 198.663 1.02153
    1792 High confidence 217.766 215.199 1.01193
    electron transfer flavoprotein alpha-subunit, mitochondrial precursor (alpha-etf). [swissprot;acc:p13804] 2049 ETFA Low confidence 186.876 183.331 1.01934
    2441 High confidence 180.137 180.732 1.0033
    electron transfer flavoprotein beta-subunit (beta-etf). [swissprot;acc:p38117] 2298 ETFB Low confidence 188.239 184.776 1.01874
    2353 High confidence 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] 1007 ETFDH Low confidence 198.075 193.349 1.02444
    2016 High confidence 199.092 197.301 1.00908
    elks protein. [refseq;acc:nm_015064] 1061 ERC1 218.162 211.648 1.03078
    2012 Low confidence 202.786 198.919 1.01944
    ell-associated factor 2; uncharacterized bone marrow protein bm040; testosterone regulated apoptosis inducer and tumor suppressor. [refseq;acc:nm_018456] 2921 EAF2 High confidence 0.00001 0.00001 1
    4522 Low confidence 210.093 208.355 1.00834
    elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [swissprot;acc:p04720] 2433 EEF1AL3 High confidence 217.366 218.117 1.00346
    3275 Low confidence 206.383 203.195 1.01569

    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/