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 Network Comparison Type Rank Gene Value Type Hugo Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 1612 to 1661 of 6456 in total
    Value Type  : Ranked
    Interaction Map  : High confidence
    Filtered  : 1
    description
    		Network Comparison Type
    		Rank
    		Hugo
    		red
    		network_comparison
    		green
    dna directed rna polymerase ii polypeptide j-related gene isoform 1; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_145325] Subtracted 839 no value 230.764 8.856 239.62
    dna directed rna polymerase ii polypeptide j-related gene isoform 3; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_032959] Divided 905 230.768 1.03841 239.632
    Subtracted 834 8.864
    dna excision repair protein ercc-1. [swissprot;acc:p07992] Divided 3216 ERCC1 0.00001 1 0.00001
    Subtracted 0 0 0
    dna fragmentation factor 40 kda subunit (ec 3.-.-.-) (dff-40) (caspase-activated deoxyribonuclease) (caspase-activated dnase) (cad) (caspase-activated nuclease) (cpan). [swissprot;acc:o76075] Divided 2515 DFFB 215.835 1.00234 216.341
    Subtracted 2512 0.506
    dna fragmentation factor alpha subunit (dna fragmentation factor 45 kda subunit) (dff-45) (inhibitor of cad) (icad). [swissprot;acc:o00273] Divided 2517 DFFA 1.00234
    Subtracted 2514 0.506
    dna ligase i (ec 6.5.1.1) (polydeoxyribonucleotide synthase [atp]). [swissprot;acc:p18858] Divided 3103 LIG1 0.00001 1 0.00001
    Subtracted 0 0 0
    dna ligase iv (ec 6.5.1.1) (polydeoxyribonucleotide synthase [atp]). [swissprot;acc:p49917] Divided 2808 LIG4 0.00001 1 0.00001
    Subtracted 0 0 0
    dna methyltransferase 1-associated protein 1 (dnmt1-associated protein 1) (dnmap1). [swissprot;acc:q9npf5] Divided 2796 DMAP1 0.00001 1 0.00001
    Subtracted 0 0 0
    dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692] Divided 1878 MLH1 212.186 1.01075 214.467
    Subtracted 1871 2.281
    dna mismatch repair protein mlh3 (mutl protein homolog 3). [swissprot;acc:q9uhc1] Divided 1749 MLH3 206.058 1.01264 203.485
    Subtracted 1772 2.573
    dna mismatch repair protein msh2. [swissprot;acc:p43246] Divided 3151 MSH2 0.00001 1 0.00001
    Subtracted 0 0 0
    dna mismatch repair protein msh6 (muts-alpha 160 kda subunit) (g/t mismatch binding protein) (gtbp) (gtmbp) (p160). [swissprot;acc:p52701] Divided 3045 MSH6 0.00001 1 0.00001
    Subtracted 0 0 0
    dna polymerase delta p38 subunit. [refseq;acc:nm_015584] Divided 1872 POLDIP2 222.819 1.01081 225.228
    Subtracted 1830 2.409
    dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] Divided 176 POLE4 275.754 1.1689 235.908
    Subtracted 112 39.846
    dna polymerase epsilon p17 subunit (dna polymerase epsilon subunit 3) (chromatin accessibility complex 17) (huchrac17) (chrac-17). [swissprot;acc:q9nrf9] Divided 1447 POLE3 250.854 1.01988 255.842
    Subtracted 1277 4.988
    dna polymerase epsilon subunit b (ec 2.7.7.7) (dna polymerase ii subunit b). [swissprot;acc:p56282] Divided 1615 POLE2 246.38 1.0156 242.596
    Subtracted 1516 3.784
    dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864] Divided 694 POLE 241.907 1.05475 229.35
    Subtracted 615 12.557
    dna polymerase gamma subunit 1 (ec 2.7.7.7) (mitochondrial dna polymerase catalytic subunit) (polg-alpha). [swissprot;acc:p54098] Divided 2074 POLG 216.324 1.00804 214.599
    Subtracted 2064 1.725
    dna repair protein rad51 homolog 1 (hrad51) (hsrad51). [swissprot;acc:q06609] Divided 2345 RAD51 219.878 1.0045 218.893
    Subtracted 2328 0.985
    dna repair protein rad52 homolog. [swissprot;acc:p43351] Divided 404 RAD52 207.908 1.08807 226.218
    Subtracted 399 18.31
    dna replication licensing factor mcm3 (dna polymerase alpha holoenzyme-associated protein p1) (rlf beta subunit) (p102 protein) (p1-mcm3). [swissprot;acc:p25205] Divided 1891 MCM3 233.828 1.01051 231.395
    Subtracted 1819 2.433
    dna replication licensing factor mcm5 (cdc46 homolog) (p1-cdc46). [swissprot;acc:p33992] Divided 1673 MCM5 228.496 1.01415 231.729
    Subtracted 1624 3.233
    dna replication licensing factor mcm8 (minichromosome maintenance 8). [swissprot;acc:q9uja3] Divided 3011 MCM8 0.00001 1 0.00001
    Subtracted 0 0 0
    dna segment on chromosome 6(unique) 2654 expressed sequence; dna segment on chromosome x (unique) 2654 expressed sequence. [refseq;acc:nm_012135] Divided 1681 FAM50B 216.899 1.01407 213.889
    Subtracted 1667 3.01
    dna topoisomerase ii, alpha isozyme (ec 5.99.1.3). [swissprot;acc:p11388] Divided 1790 no value 203.759 1.01197 201.349
    Subtracted 1825 2.41
    dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880] Divided 1796 TOP2B 1.01193 201.357

    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/