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 1112 to 1161 of 66312 in total
    Filtered  : 1
    description
    		Rank
    		Hugo
    		Network Comparison Type
    		Value Type
    		Interaction Map
    		red
    		green
    		network_comparison
    40s ribosomal protein s11. [swissprot;acc:p04643] 4910 RPS11 Subtracted Rooted Low confidence 68.7371 69.4847 0.7476
    40s ribosomal protein s12. [swissprot;acc:p25398] 3133 no value Divided Squared 43974.9 42497.6 1.03476
    3226 Subtracted 1477.3
    3276 Divided Measured 7785.76 7995.94 1.027
    3415 Subtracted 210.18
    3859 Divided Rooted 70.9166 72.9222 1.02828
    3917 Subtracted 2.0056
    4261 Divided Ranked 203.546 201.631 1.0095
    Subtracted 1.915
    40s ribosomal protein s13. [swissprot;acc:q02546] 776 RPS13 Divided Squared High confidence 21976 25607.9 1.16527
    936 Subtracted 3631.9
    1498 Divided Measured 5414.98 5818.7 1.07456
    1677 Subtracted 403.72
    1695 Ranked 220.899 223.813 2.914
    1722 Divided 1.01319
    2348 Rooted 60.5137 61.6019 1.01798
    2361 Subtracted 1.0882
    2785 Measured Low confidence 8031.31 8262.44 231.13
    2851 Divided 1.02878
    3388 Subtracted Rooted 72.0347 74.2382 2.2035
    3405 Divided 1.03059
    3490 Subtracted Squared 45834.3 44427.7 1406.6
    3619 Divided 1.03166
    3777 Ranked 201.886 199.227 1.01335
    3787 Subtracted 2.659
    40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366] 323 RPS14 High confidence 242.238 264.11 21.872
    386 Divided 1.09029
    530 Rooted 50.6537 46.6413 1.08603
    824 Subtracted 4.0124
    1823 Divided Squared 13145.4 14424.1 1.09727
    2030 Low confidence 41640.7 40034.4 1.04012
    2418 Subtracted High confidence 13145.4 14424.1 1278.7
    2436 Divided Measured 3708.67 3584.47 1.03465
    2520 Subtracted 124.2
    2658 Squared Low confidence 41640.7 40034.4 1606.3
    4334 Divided Measured 7425.75 7571.79 1.01967
    4511 Subtracted 146.04
    4684 Ranked 208.268 209.433 1.165
    4717 Divided 1.00559
    4747 Rooted 68.8727 70.0583 1.01721
    4761 Subtracted 1.1856
    40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] 219 no value Ranked High confidence 242.339 266.986 24.647
    304 Divided 1.1017
    376 Rooted 50.2554 45.5688 1.10285
    651 Subtracted 4.6866
    1989 Divided Squared 12388.6 13523.5 1.09161
    2067 Measured 3602.75 3411.18 1.05616
    2391 Subtracted 191.57
    2497 Squared 12388.6 13523.5 1134.9
    2567 Divided Low confidence 41752.3 40220.1 1.0381

    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/