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 [...,...].
    Filtered description Gene Value Type Rank Network Comparison Type network_comparison Interaction Map green red
    Results: HTML CSV LaTeX Showing element 1001 to 1050 of 77072 in total
    Filtered  : 0
    description
    		Value Type
    		Rank
    		Network Comparison Type
    		network_comparison
    		Interaction Map
    		green
    		red
    alpha 2 globin. [refseq;acc:nm_000517] Measured 602 Divided 1.03569 Low confidence 1066.67 1104.74
    643 Subtracted 38.07
    Ranked 19 4500.9 15987.1 11486.2
    30 Divided 1.39185
    Squared 281 Subtracted 631.92 7479.85 6847.93
    545 Divided 1.09228
    Rooted 53 Subtracted 5.4015 12.9538 18.3553
    67 Divided 1.41698
    alpha crystallin a chain. [swissprot;acc:p02489] Measured 86 1.61366 High confidence 89.2447 55.3059
    390 Subtracted 33.9388
    559 57.45 Low confidence 1749.08 1806.53
    619 Divided 1.03285
    Ranked 86 Subtracted 2400.2 High confidence 13972.2 16372.4
    139 Divided 1.17178
    656 1.02341 Low confidence 11069.9 11329
    661 Subtracted 259.1
    Squared 121 Divided 1.89488 High confidence 2.40686 1.27019
    371 Subtracted 360.79 Low confidence 7807.66 7446.87
    444 1.13667 High confidence 2.40686 1.27019
    664 Divided 1.04845 Low confidence 7807.66 7446.87
    Rooted 68 1.38766 High confidence 8.63381 6.22183
    239 Subtracted 2.41198
    565 Divided 1.04168 Low confidence 24.6113 25.637
    575 Subtracted 1.0257
    alpha-1-acid glycoprotein 2 precursor (agp 2) (orosomucoid 2) (omd 2). [swissprot;acc:p19652] Measured 435 16.74 High confidence 2335.98 2319.24
    475 Divided 1.00722
    496 Subtracted 75.49 Low confidence 1742.4 1817.89
    577 Divided 1.04333
    Ranked 215 Subtracted 1190 11679.4 10489.4
    309 Divided 1.11345
    418 Subtracted 319.7 High confidence 10866.3 11186
    421 Divided 1.02942
    Squared 279 Subtracted 108.26 3670.49 3778.75
    444 Divided 1.02949
    602 Subtracted 91.53 Low confidence 2700.46 2791.99
    709 Divided 1.03389
    Rooted 333 Subtracted 2.3937 26.6816 29.0753
    381 Divided 1.08971
    405 Subtracted 0.7178 High confidence 32.9629 32.2451
    447 Divided 1.02226
    alpha-amylase, salivary precursor (ec 3.2.1.1) (1,4-alpha-d-glucan glucanohydrolase). [swissprot;acc:p04745] Measured 430 Subtracted 103.56 Low confidence 2105.24 2208.8
    432 103.26 2308.49 2205.23
    566 Divided 1.04919 2105.24 2208.8
    571 1.04683 2308.49 2205.23
    Ranked 122 Subtracted 1877.4 13113.5 11236.1
    133 Divided 1.16709
    331 Subtracted 818.61 10670.2 9851.59
    392 Divided 1.08309
    Squared 171 Subtracted 1312.68 11288.3 9975.62
    354 Divided 1.13159

    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
    - 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/