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 273 to 322 of 8289 in total
    Network Comparison Type  : Divided
    Value Type  : Ranked
    Filtered  : 1
    description
    		Rank
    		Hugo
    		Interaction Map
    		red
    		green
    		network_comparison
    60s ribosomal protein l13 (breast basic conserved protein 1). [swissprot;acc:p26373] 3643 RPL13 Low confidence 203.892 201.053 1.01412
    60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1] 390 MRPL13 High confidence 241.828 263.62 1.09011
    4867 Low confidence 206.138 205.562 1.0028
    60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429] 392 RPL13A High confidence 241.83 263.615 1.09008
    4738 Low confidence 206.344 207.457 1.00539
    60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914] 306 no value High confidence 242.153 266.673 1.10126
    4097 Low confidence 202.12 199.957 1.01082
    60s ribosomal protein l15. [swissprot;acc:p39030] 604 RPL15 High confidence 217.862 230.978 1.0602
    4877 Low confidence 202.236 201.713 1.00259
    60s ribosomal protein l17 (l23). [swissprot;acc:p18621] 281 no value High confidence 241.808 267.335 1.10557
    4212 Low confidence 206.899 208.987 1.01009
    60s ribosomal protein l18. [swissprot;acc:q07020] 485 RPL18 High confidence 237.109 254.667 1.07405
    4209 Low confidence 205.452 203.391 1.01013
    60s ribosomal protein l18a. [swissprot;acc:q02543] 860 no value High confidence 234.025 224.958 1.04031
    2022 Low confidence 201.763 197.919 1.01942
    60s ribosomal protein l19. [swissprot;acc:p14118] 319 RPL19 High confidence 240.73 264.729 1.09969
    4578 Low confidence 206.719 208.289 1.00759
    60s ribosomal protein l21. [swissprot;acc:p46778] 1054 no value High confidence 223.958 217.263 1.03082
    4501 Low confidence 198.901 197.192 1.00867
    60s ribosomal protein l22 (epstein-barr virus small rna associated protein) (eber associated protein) (eap) (heparin binding protein hbp15). [swissprot;acc:p35268] 2205 High confidence 199.129 200.413 1.00645
    4593 Low confidence 204.498 203.022 1.00727
    60s ribosomal protein l23 (l17). [swissprot;acc:p23131] 293 High confidence 240.782 265.717 1.10356
    4684 Low confidence 205.529 206.721 1.0058
    60s ribosomal protein l23a. [swissprot;acc:p29316] 323 High confidence 241.884 265.945 1.09947
    4167 Low confidence 207.351 209.511 1.01042
    60s ribosomal protein l24 (l30). [swissprot;acc:p38663] 1767 RPL24 High confidence 201.288 198.86 1.01221
    3921 Low confidence 203.414 200.897 1.01253
    60s ribosomal protein l26. [swissprot;acc:q02877] 302 RPL26 High confidence 242.326 267.008 1.10185
    4505 Low confidence 207.061 208.837 1.00858
    60s ribosomal protein l27. [swissprot;acc:p08526] 197 RPL27 211.912 201.556 1.05138
    60s ribosomal protein l28. [swissprot;acc:p46779] 1882 RPL28 High confidence 215.896 213.61 1.0107
    2733 Low confidence 203.065 199.576 1.01748
    60s ribosomal protein l29 (cell surface heparin binding protein hip). [swissprot;acc:p47914] 169 RPL29 216.79 205.07 1.05715
    2664 High confidence 204.768 204.549 1.00107
    60s ribosomal protein l3-like. [swissprot;acc:q92901] 312 RPL3L 242.195 266.663 1.10103
    4635 Low confidence 207.074 208.441 1.0066
    60s ribosomal protein l30. [swissprot;acc:p04645] 378 RPL30 High confidence 242.593 265.365 1.09387
    3430 Low confidence 207.855 204.741 1.01521
    60s ribosomal protein l31. [swissprot;acc:p12947] 862 RPL31 High confidence 234.025 224.958 1.04031
    2345 Low confidence 201.98 198.29 1.01861
    60s ribosomal protein l32, mitochondrial precursor (l32mt) (hspc283). [swissprot;acc:q9byc8] 4034 MRPL32 203.062 200.757 1.01148
    60s ribosomal protein l32. [swissprot;acc:p02433] 276 SNORA7A High confidence 241.13 266.969 1.10716
    3156 Low confidence 207.568 210.937 1.01623
    60s ribosomal protein l34, mitochondrial precursor (l34mt). [swissprot;acc:q9bq48] 1333 MRPL34 High confidence 220.681 215.78 1.02271
    3852 Low confidence 204.301 201.678 1.01301
    60s ribosomal protein l34. [swissprot;acc:p49207] 308 RPL34 High confidence 242.153 266.673 1.10126
    4903 Low confidence 204.23 204.633 1.00197
    60s ribosomal protein l35. [swissprot;acc:p42766] 303 RPL35 High confidence 242.333 266.999 1.10179
    4224 Low confidence 206.836 208.898 1.00997
    60s ribosomal protein l35a. [swissprot;acc:p18077] 2451 RPL35A 200.987 197.369 1.01833

    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/