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 red Interaction Map Filtered network_comparison green
    Results: HTML CSV LaTeX Showing element 2012 to 2061 of 66312 in total
    Filtered  : 1
    description
    		Rank
    		Hugo
    		Network Comparison Type
    		Value Type
    		red
    		Interaction Map
    		network_comparison
    		green
    60 kda tat interactive protein (tip60) (hiv-1 tat interactive protein) (cpla(2) interacting protein). [swissprot;acc:q92993] 3686 HTATIP Divided Rooted 72.4895 Low confidence 1.0293 74.6137
    3722 Ranked 200.338 1.01359 197.651
    3751 Subtracted 2.687
    3889 Measured 8092.22 187.12 8279.34
    3927 Divided 1.02312
    60s acidic ribosomal protein p0 (l10e). [swissprot;acc:p05388] 1022 RPLP0 Subtracted Ranked 226.203 High confidence 6.652 232.855
    1092 Divided 1.02941
    2112 Subtracted Squared 22719.3 1862.2 24581.5
    2254 Divided 1.08197
    2258 Measured 5150.31 1.04616 5388.05
    2317 Subtracted 237.74
    2433 Squared 45529.4 Low confidence 1657.4 43872
    2627 Divided 1.03778
    2720 Rooted 58.3416 High confidence 1.00112 58.4068
    2730 Subtracted 0.0652
    3356 Measured 7970.4 Low confidence 212.08 8182.48
    3362 Divided 1.02661
    3614 Rooted 71.7525 1.02965 73.8799
    3645 Subtracted 2.1274
    3894 Ranked 202.202 2.529 199.673
    3897 Divided 1.01267
    60s acidic ribosomal protein p1. [swissprot;acc:p05386] 831 no value Subtracted 229.171 High confidence 8.877 238.048
    898 Divided 1.03874
    2014 Squared 44220.4 Low confidence 1.04023 42510.4
    2220 Subtracted 1710
    2296 20706.1 High confidence 1555.8 22261.9
    2326 Divided 1.07514
    2409 Subtracted Measured 4857.03 182.75 5039.78
    2418 Divided 1.03763
    2564 Rooted 56.832 1.00907 56.3214
    2591 Subtracted 0.5106
    4462 Divided Measured 7814.23 Low confidence 1.01918 7964.08
    4475 Subtracted 149.85
    4638 Divided Rooted 71.0892 1.01986 72.5008
    4659 Subtracted 1.4116
    4994 Divided Ranked 203.12 1.00034 203.189
    Subtracted 0.069
    60s acidic ribosomal protein p2. [swissprot;acc:p05387] 621 RPLP2 231.92 High confidence 12.515 244.435
    720 Divided 1.05396
    1403 Squared 45268.2 Low confidence 1.04404 43358.7
    1497 Subtracted 1909.5
    1708 Divided Rooted 56.1247 High confidence 1.03266 54.3497
    1863 Subtracted Ranked 204.808 Low confidence 3.922 200.886
    1974 Rooted 56.1247 High confidence 1.775 54.3497
    1982 Divided Ranked 204.808 Low confidence 1.01952 200.886
    2517 Rooted 71.0067 1.03357 73.3902
    2685 Subtracted 2.3835
    2743 Divided Measured 4824.49 High confidence 1.0022 4813.92
    2744 Subtracted 10.57
    2745 Divided Squared 21770.6 1.00342 21696.3

    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/