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 Network Comparison Type Gene Value Type Hugo Interaction Map red Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 3180 to 3229 of 66312 in total
    Filtered  : 1
    description
    		Rank
    		Network Comparison Type
    		Value Type
    		Hugo
    		Interaction Map
    		red
    		green
    		network_comparison
    actin binding lim protein 2. [refseq;acc:nm_032432] 1937 Subtracted Squared ABLIM2 High confidence 28264.4 30386.4 2122
    2127 Measured Low confidence 7670 7921.78 251.78
    2332 Divided Squared High confidence 28264.4 30386.4 1.07508
    3513 Low confidence 43742.1 42371.9 1.03234
    3597 Subtracted 1370.2
    actin, alpha cardiac. [swissprot;acc:p04270] 914 ACTC1 45895 43771.9 2123.1
    966 Divided 1.0485
    3923 Subtracted Rooted 72.384 74.3873 2.0033
    3960 Divided 1.02768
    3962 Ranked 200.879 198.479 1.01209
    3973 Subtracted 2.4
    4021 Divided Measured 8073.06 8251.68 1.02213
    4148 Subtracted 178.62
    actin, aortic smooth muscle (alpha-actin 2). [swissprot;acc:p03996] 917 Squared ACTA2 45894.9 43772 2122.9
    967 Divided 1.0485
    3924 Subtracted Rooted 72.3846 74.3879 2.0033
    3961 Divided 1.02768
    3964 Ranked 200.877 198.477 1.01209
    3974 Subtracted 2.4
    4022 Divided Measured 8073.12 8251.74 1.02213
    4149 Subtracted 178.62
    actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571] 1206 Squared ACTG1 High confidence 28554.8 31619.6 3064.8
    1280 Measured 6036.22 6512.64 476.42
    1284 Rooted 63.0056 65.7244 2.7188
    1307 Divided 1.04315
    1354 Measured 6036.22 6512.64 1.07893
    1529 Ranked 216.762 213.031 1.01751
    1536 Subtracted 3.731
    1636 Divided Squared 28554.8 31619.6 1.10733
    1671 Low confidence 45216.3 43374.8 1.04246
    1737 Subtracted 1841.5
    3385 Measured 8001.89 8213.1 211.21
    3418 Divided 1.0264
    3425 Subtracted Rooted 72.1822 74.3776 2.1954
    3454 Divided 1.03041
    3630 Ranked 200.633 197.828 1.01418
    3638 Subtracted 2.805
    actin, gamma-enteric smooth muscle (alpha-actin 3). [swissprot;acc:p12718] 916 Squared ACTG2 45894.9 43772 2122.9
    965 Divided 1.0485
    3922 Subtracted Rooted 72.3846 74.3879 2.0033
    3959 Divided 1.02768
    3961 Ranked 200.877 198.477 1.01209
    3972 Subtracted 2.4
    4020 Divided Measured 8073.12 8251.74 1.02213
    4147 Subtracted 178.62
    actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [refseq;acc:nm_002313] 629 Rooted ABLIM1 High confidence 60.0129 64.7371 4.7242
    633 Ranked 229.072 216.576 12.496
    640 Divided Rooted 60.0129 64.7371 1.07872
    668 Ranked 229.072 216.576 1.0577
    776 Subtracted Low confidence 208.488 203.181 5.307

    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/