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 Gene Hugo Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 251 to 300 of 8289 in total
    Network Comparison Type  : Divided
    Value Type  : Ranked
    Filtered  : 1
    description
    		Rank
    		Hugo
    		Interaction Map
    		red
    		green
    		network_comparison
    60 kda tat interactive protein (tip60) (hiv-1 tat interactive protein) (cpla(2) interacting protein). [swissprot;acc:q92993] 826 HTATIP High confidence 223.186 213.912 1.04335
    3722 Low confidence 200.338 197.651 1.01359
    60s acidic ribosomal protein p0 (l10e). [swissprot;acc:p05388] 1092 RPLP0 High confidence 226.203 232.855 1.02941
    3897 Low confidence 202.202 199.673 1.01267
    60s acidic ribosomal protein p1. [swissprot;acc:p05386] 898 no value High confidence 229.171 238.048 1.03874
    4994 Low confidence 203.12 203.189 1.00034
    60s acidic ribosomal protein p2. [swissprot;acc:p05387] 720 RPLP2 High confidence 231.92 244.435 1.05396
    1982 Low confidence 204.808 200.886 1.01952
    60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] 357 no value High confidence 243.12 266.661 1.09683
    4740 Low confidence 207.452 208.569 1.00538
    60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025] 356 High confidence 243.24 266.796 1.09684
    4858 Low confidence 207.503 208.103 1.00289
    60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [swissprot;acc:q9y3b7] 373 MRPL11 High confidence 242.37 265.255 1.09442
    4601 Low confidence 208.668 210.165 1.00717
    60s ribosomal protein l11. [swissprot;acc:p39026] 283 RPL11 High confidence 241.828 267.346 1.10552
    2678 Low confidence 208.542 212.217 1.01762
    60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] 338 no value High confidence 243.583 267.528 1.0983
    4667 Low confidence 206.86 208.125 1.00612
    60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815] 369 MRPL12 High confidence 242.159 265.104 1.09475
    3886 Low confidence 204.522 201.949 1.01274
    60s ribosomal protein l12. [swissprot;acc:p30050] 337 no value High confidence 243.583 267.527 1.0983
    4669 Low confidence 206.837 208.096 1.00609
    60s ribosomal protein l13 (breast basic conserved protein 1). [swissprot;acc:p26373] 3643 RPL13 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

    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/