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 59874 to 59923 of 66312 in total
    Filtered  : 1
    description
    		Rank
    		Hugo
    		Network Comparison Type
    		Value Type
    		Interaction Map
    		red
    		green
    		network_comparison
    trs85 homolog. [swissprot;acc:q9y2l5] 47 KIAA1012 Subtracted Measured High confidence 24896.4 20431.7 4464.7
    98 Divided Squared 227160 146079 1.55505
    202 Subtracted Rooted 138.375 127.926 10.449
    259 Divided Squared Low confidence 50448.8 46264.1 1.09045
    261 Subtracted 4184.7
    263 Divided Measured High confidence 24896.4 20431.7 1.21852
    600 Rooted 138.375 127.926 1.08168
    851 Ranked 107.842 112.329 1.04161
    1371 Subtracted 4.487
    4150 Divided Low confidence 200.724 198.625 1.01057
    4164 Subtracted 2.099
    4448 Rooted 73.2039 74.9037 1.6998
    4466 Divided 1.02322
    4887 Subtracted Measured 8389.61 8450.36 60.75
    4890 Divided 1.00724
    trub pseudouridine (psi) synthase homolog 1. [refseq;acc:nm_139169] 383 TRUB1 Subtracted Ranked High confidence 236.245 255.113 18.868
    431 Divided 1.07987
    859 Rooted 53.3429 50.2017 1.06257
    1091 Subtracted 3.1412
    1309 Divided Squared 15397.3 17378.3 1.12866
    2032 Subtracted 1981
    2671 Divided Low confidence 40982.2 39502.1 1.03747
    2698 Measured High confidence 4163.36 4145.95 1.0042
    2736 Subtracted 17.41
    3212 Squared Low confidence 40982.2 39502.1 1480.1
    3944 Ranked 209.294 211.763 2.469
    3995 Divided 1.0118
    4582 Measured 7337.1 7463.75 1.01726
    4654 Subtracted 126.65
    4866 Divided Rooted 68.4055 69.266 1.01258
    4874 Subtracted 0.8605
    trypsin i precursor (ec 3.4.21.4) (cationic trypsinogen). [swissprot;acc:p07477] 12 PRSS1 Divided 32.2966 47.9763 1.48549
    Subtracted Ranked 304.359 246.737 57.622
    15 Divided Measured 1983.91 3007.85 1.51612
    19 Subtracted Rooted 32.2966 47.9763 15.6797
    20 Divided Ranked 304.359 246.737 1.23354
    69 Subtracted Measured 1983.91 3007.85 1023.94
    4591 Divided Squared 9206.82 9374.99 1.01827
    4947 Subtracted 168.17
    trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [swissprot;acc:p35030] 11 PRSS3 Divided Rooted 32.2231 47.928 1.48738
    Subtracted Ranked 304.548 246.824 57.724
    14 Divided Measured 1972.65 2998.1 1.51983
    18 Subtracted Rooted 32.2231 47.928 15.7049
    19 Divided Ranked 304.548 246.824 1.23387
    68 Subtracted Measured 1972.65 2998.1 1025.45
    4576 Divided Squared 9136.66 9308.54 1.01881
    4945 Subtracted 171.88
    tryptophan 2,3-dioxygenase (ec 1.13.11.11) (tryptophan pyrrolase) (tryptophanase) (tryptophan oxygenase) (tryptamin 2,3-dioxygenase) (trpo). [swissprot;acc:p48775] 541 TDO2 Divided Rooted 71.0407 74.1958 1.04441
    564 Subtracted 3.1551
    638 Divided Measured 7720 8065.07 1.0447

    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/