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 Network Comparison Type Hugo Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2632 to 2681 of 6456 in total
    Value Type  : Ranked
    Interaction Map  : High confidence
    Filtered  : 1
    description
    		Rank
    		Network Comparison Type
    		Hugo
    		red
    		green
    		network_comparison
    hmg2 like. [refseq;acc:nm_145205] 2799 Subtracted HMGB4 0 0 0
    homeobox prospero-like protein prox1 (prox 1). [swissprot;acc:q92786] 2194 Divided PROX1 209.54 208.162 1.00662
    2209 Subtracted 1.378
    homeobox protein barh-like 1. [swissprot;acc:q9hbu1] 499 BARX1 237.28 252.492 15.212
    582 Divided 1.06411
    homeobox protein barh-like 2. [swissprot;acc:q9umq3] 504 Subtracted BARX2 15.212
    587 Divided 1.06411
    homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] 557 CUTL2 207.272 194.371 1.06637
    604 Subtracted 12.901
    homeobox protein dlx-2. [swissprot;acc:q07687] 2313 DLX2 229.258 230.294 1.036
    2337 Divided 1.00452
    homeobox protein dlx-3. [swissprot;acc:o60479] 2316 Subtracted DLX3 1.036
    2340 Divided 1.00452
    homeobox protein dlx-5. [swissprot;acc:p56178] 2314 Subtracted DLX5 1.036
    2338 Divided 1.00452
    homeobox protein engrailed-2 (hu-en-2). [swissprot;acc:p19622] 1135 Subtracted EN2 219.399 213.784 5.615
    1167 Divided 1.02626
    homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 1 Subtracted HLX 215 322 107
    7 Divided 1.49767
    homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [swissprot;acc:p31260] 614 HOXA10 214.257 202.125 1.06002
    647 Subtracted 12.132
    homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 686 Divided no value 132.413 125.389 1.05602
    975 Subtracted 7.024
    homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] 685 Divided HOXA5 1.05602
    974 Subtracted 7.024
    homeobox protein hox-a9 (hox-1g). [swissprot;acc:p31269] 616 Divided HOXA9 214.257 202.132 1.05999
    649 Subtracted 12.125
    homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] 680 Divided HOXB4 132.413 125.389 1.05602
    969 Subtracted 7.024
    homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] 684 Divided HOXB5 1.05602
    973 Subtracted 7.024
    homeobox protein hox-b9 (hox-2e) (hox-2.5). [swissprot;acc:p17482] 615 Divided HOXB9 214.257 202.132 1.05999
    648 Subtracted 12.125
    homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 679 Divided no value 132.413 125.389 1.05602
    968 Subtracted 7.024
    homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] 681 Divided HOXC5 1.05602
    970 Subtracted 7.024
    homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 682 Divided no value 1.05602
    971 Subtracted 7.024
    homeobox protein hox-c9 (hox-3b). [swissprot;acc:p31274] 617 Divided HOXC9 214.257 202.135 1.05997
    650 Subtracted 12.122
    homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] 683 Divided HOXD4 132.413 125.389 1.05602
    972 Subtracted 7.024
    homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356] 632 Divided HOXD9 214.254 202.166 1.05979
    665 Subtracted 12.088
    homeobox protein meis1. [swissprot;acc:o00470] 1783 Divided MEIS1 206.332 203.874 1.01206
    1807 Subtracted 2.458
    homeobox protein meis2 (meis1-related protein 1). [swissprot;acc:o14770] 1784 Divided MEIS2 1.01206
    1808 Subtracted 2.458
    homeobox protein meis3 (meis1-related protein 2) (fragment). [swissprot;acc:q99687] 1788 Divided MEIS3 1.01206

    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/