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 158 to 207 of 8289 in total
    Network Comparison Type  : Divided
    Value Type  : Ranked
    Filtered  : 1
    description
    		Rank
    		Hugo
    		Interaction Map
    		red
    		green
    		network_comparison
    40s ribosomal protein s20. [swissprot;acc:p17075] 342 RPS20 High confidence 243.5 267.21 1.09737
    4957 Low confidence 207.359 207.585 1.00109
    40s ribosomal protein s21. [swissprot;acc:p35265] 790 RPS21 High confidence 224.244 234.511 1.04578
    3794 Low confidence 202.443 199.787 1.01329
    40s ribosomal protein s23. [swissprot;acc:p39028] 324 RPS23 High confidence 243.944 268.195 1.09941
    4531 Low confidence 209.371 211.088 1.0082
    40s ribosomal protein s24 (s19). [swissprot;acc:p16632] 1690 RPS24 High confidence 224.091 227.184 1.0138
    4880 Low confidence 204.152 204.674 1.00256
    40s ribosomal protein s25. [swissprot;acc:p25111] 1980 RPS25 206.198 202.249 1.01953
    40s ribosomal protein s26. [swissprot;acc:p02383] 454 no value High confidence 210.224 226.578 1.07779
    4266 Low confidence 202.198 204.106 1.00944
    40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677] 1102 High confidence 229.442 235.974 1.02847
    3981 Low confidence 203.072 200.675 1.01194
    40s ribosomal protein s27a. [swissprot;acc:p14798] 3486 RPS27A 202.475 199.484 1.01499
    40s ribosomal protein s28. [swissprot;acc:p25112] 1982 no value High confidence 200.343 198.427 1.00966
    2356 Low confidence 201.372 197.696 1.01859
    40s ribosomal protein s29. [swissprot;acc:p30054] 277 High confidence 241.849 267.642 1.10665
    3809 Low confidence 206.222 208.959 1.01327
    40s ribosomal protein s3. [swissprot;acc:p23396] 346 RPS3 High confidence 241.612 265.119 1.09729
    4895 Low confidence 207.078 207.531 1.00219
    40s ribosomal protein s30. [swissprot;acc:q05472] 1081 FAU High confidence 223.44 216.875 1.03027
    2714 Low confidence 202.521 199.033 1.01752
    40s ribosomal protein s3a. [swissprot;acc:p49241] 867 no value High confidence 225.689 234.674 1.03981
    4226 Low confidence 203.416 201.41 1.00996
    40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] 288 High confidence 240.758 266.078 1.10517
    1593 Low confidence 208.892 213.282 1.02102
    40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] 287 RPS4Y2 High confidence 240.758 266.079 1.10517
    1580 Low confidence 208.899 213.298 1.02106
    40s ribosomal protein s5. [swissprot;acc:p46782] 366 RPS5 High confidence 242.473 265.756 1.09602
    4831 Low confidence 207.559 208.333 1.00373
    40s ribosomal protein s7 (s8). [swissprot;acc:p23821] 1594 RPS7 205.505 201.279 1.021
    2149 High confidence 217.871 219.366 1.00686
    40s ribosomal protein s8. [swissprot;acc:p09058] 1397 RPS8 218.64 214.049 1.02145
    2283 Low confidence 200.909 197.203 1.01879
    40s ribosomal protein s9. [swissprot;acc:p46781] 439 RPS9 High confidence 238.986 257.784 1.07866
    4679 Low confidence 204.824 203.621 1.00591
    40s ribosomal protein sa (p40) (34/67 kda laminin receptor) (colon carcinoma laminin-binding protein) (nem/1chd4) (multidrug resistance- associated protein mgr1-ag). [swissprot;acc:p08865] 789 no value High confidence 224.244 234.511 1.04578
    4099 Low confidence 202.893 200.728 1.01079
    43 kda receptor-associated protein of the synapse (rapsyn) (acetylcholine receptor-associated 43 kda protein) (43 kda postsynaptic protein). [swissprot;acc:q13702] 2232 RAPSN High confidence 215.547 214.194 1.00632
    2906 Low confidence 202.663 199.268 1.01704
    44050 protein. [refseq;acc:nm_178832] 2506 C10orf83 High confidence 151.386 151.009 1.0025
    3824 Low confidence 199.574 196.978 1.01318
    45 kda calcium-binding protein precursor (cab45) (stromal cell-derived factor 4) (sdf-4). [swissprot;acc:q9brk5] 2147 SDF4 High confidence 206.442 207.862 1.00688
    2500 Low confidence 198.748 195.198 1.01819
    5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478] 879 PRKAB1 High confidence 212.002 203.954 1.03946
    2381 Low confidence 201.395 197.73 1.01854
    5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741] 877 PRKAB2 High confidence 212.002 203.954 1.03946
    2351 Low confidence 201.408 197.731 1.0186
    5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131] 876 PRKAA1 High confidence 212.002 203.954 1.03946
    1683 Low confidence 200.836 196.78 1.02061

    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/