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 64824 to 64873 of 66312 in total
    Filtered  : 1
    description
    		Rank
    		Network Comparison Type
    		Value Type
    		Hugo
    		Interaction Map
    		red
    		green
    		network_comparison
    zinc finger protein 206. [refseq;acc:nm_032805] 4401 Subtracted Ranked ZSCAN10 Low confidence 197.793 195.963 1.83
    zinc finger protein 207. [swissprot;acc:o43670] 1169 Divided Measured ZNF207 High confidence 5470.44 5949.49 1.08757
    1216 Rooted 60.2183 62.9735 1.04575
    1267 Subtracted Measured 5470.44 5949.49 479.05
    1271 Rooted 60.2183 62.9735 2.7552
    1605 Ranked 221.934 218.658 3.276
    1633 Divided 1.01498
    1668 Subtracted Squared 24216.1 26647.5 2431.4
    1765 Divided 1.1004
    2835 Subtracted Measured Low confidence 8036.53 8266.09 229.56
    2891 Divided 1.02856
    3187 Subtracted Squared 45914.4 44427.3 1487.1
    3212 Rooted 72.0362 74.2988 2.2626
    3217 Divided 1.03141
    3355 Squared 45914.4 44427.3 1.03347
    3550 Subtracted Ranked 201.913 199.002 2.911
    3554 Divided 1.01463
    zinc finger protein 208. [swissprot;acc:o43345] 1049 Subtracted Squared no value 56615.7 54513.3 2102.4
    2424 Divided 1.03857
    4096 Subtracted Measured 9143.35 9323.2 179.85
    4231 Rooted 76.1821 78.0464 1.8643
    4361 Divided 1.02447
    4390 Measured 9143.35 9323.2 1.01967
    4393 Ranked 197.793 195.963 1.00934
    4411 Subtracted 1.83
    zinc finger protein 211 (zinc finger protein c2h2-25). [swissprot;acc:q13398] 1047 Squared ZNF211 56615.7 54513.3 2102.4
    2422 Divided 1.03857
    4127 Subtracted Measured 9143.35 9323.19 179.84
    4229 Rooted 76.1821 78.0464 1.8643
    4359 Divided 1.02447
    4388 Measured 9143.35 9323.19 1.01967
    4390 Ranked 197.793 195.963 1.00934
    4409 Subtracted 1.83
    zinc finger protein 213 (putative transcription factor cr53). [swissprot;acc:o14771] 873 ZNF213 High confidence 269.954 278.217 8.263
    1061 Divided Squared Low confidence 43583 41617.4 1.04723
    1072 Ranked High confidence 269.954 278.217 1.03061
    1363 Subtracted Squared Low confidence 43583 41617.4 1965.6
    2482 Divided Measured High confidence 3568.99 3676.61 1.03015
    2542 Subtracted 107.62
    2659 Divided Squared 17924.3 17435.9 1.02801
    2666 Subtracted 488.4
    2699 Divided Rooted 44.5861 44.443 1.00322
    2706 Subtracted 0.1431
    4064 Divided Measured Low confidence 7595.78 7761.21 1.02178
    4309 Subtracted 165.43
    4476 Divided Rooted 69.1953 70.7973 1.02315
    4532 Subtracted 1.602
    4933 Ranked 209.176 208.915 0.261
    4934 Divided 1.00125
    zinc finger protein 214 (bwscr2 associated zinc-finger protein 1) (baz 1). [swissprot;acc:q9ul59] 1020 Subtracted Squared ZNF214 56615.7 54513.3 2102.4

    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/