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 red Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 2101 to 2150 of 66312 in total
    Filtered  : 1
    description
    		Rank
    		Hugo
    		Network Comparison Type
    		Value Type
    		Interaction Map
    		red
    		green
    		network_comparison
    60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [swissprot;acc:q9y3b7] 1743 MRPL11 Divided Squared High confidence 12299.6 13539.1 1.10078
    2417 Measured 3598.55 3467.65 1.03775
    2438 Subtracted Squared 12299.6 13539.1 1239.5
    2515 Measured 3598.55 3467.65 130.9
    2540 Divided Squared Low confidence 41209.5 39690.7 1.03827
    3044 Subtracted 1518.8
    4257 Divided Measured 7371.06 7516.3 1.0197
    4520 Subtracted 145.24
    4582 Ranked 208.668 210.165 1.497
    4601 Divided 1.00717
    4785 Rooted 68.6271 69.7331 1.01612
    4799 Subtracted 1.106
    60s ribosomal protein l11. [swissprot;acc:p39026] 201 RPL11 Ranked High confidence 241.828 267.346 25.518
    283 Divided 1.10552
    336 Rooted 50.3167 45.4063 1.10814
    586 Subtracted 4.9104
    1551 Divided Squared Low confidence 40796.2 39112.9 1.04304
    1834 Measured High confidence 3593.24 3375.93 1.06437
    2108 Squared 12200.6 13277 1.08823
    2323 Subtracted Ranked Low confidence 208.542 212.217 3.675
    2344 Squared 40796.2 39112.9 1683.3
    2352 Measured High confidence 3593.24 3375.93 217.31
    2529 Squared 12200.6 13277 1076.4
    2678 Divided Ranked Low confidence 208.542 212.217 1.01762
    4791 Measured 7310.03 7393.1 1.01136
    4809 Subtracted 83.07
    4931 Divided Rooted 68.4157 68.9736 1.00815
    4936 Subtracted 0.5579
    60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] 246 no value Ranked High confidence 243.583 267.528 23.945
    338 Divided 1.0983
    407 Rooted 49.9856 45.4431 1.09996
    683 Subtracted 4.5425
    1933 Divided Squared 12442.9 13606.8 1.09354
    2186 Measured 3586.3 3414.4 1.05035
    2432 Subtracted 171.9
    2488 Squared 12442.9 13606.8 1163.9
    2565 Divided Low confidence 40546.7 39057.1 1.03814
    3166 Subtracted 1489.6
    3916 Divided Measured 7342.34 7512.91 1.02323
    4241 Subtracted 170.57
    4651 Ranked 206.86 208.125 1.265
    4667 Divided 1.00612
    4684 Rooted 68.8421 70.1162 1.01851
    4734 Subtracted 1.2741
    60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815] 281 MRPL12 Ranked High confidence 242.159 265.104 22.945
    369 Divided 1.09475
    489 Rooted 50.5505 46.2797 1.09228
    757 Subtracted 4.2708
    1878 Divided Squared 12933 14159.6 1.09484
    2372 Measured 3677.53 3526.65 1.04278

    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/