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 1630 to 1679 of 8289 in total
    Network Comparison Type  : Divided
    Value Type  : Ranked
    Filtered  : 1
    description
    		Rank
    		Hugo
    		Interaction Map
    		red
    		green
    		network_comparison
    crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] 564 CRNKL1 High confidence 220.744 207.121 1.06577
    cryptochrome 1 (photolyase-like). [refseq;acc:nm_004075] 1274 CRY1 Low confidence 193.539 189.282 1.02249
    ctcl tumor antigen l14-2. [refseq;acc:nm_018017] 2677 C10orf118 203.566 200.041 1.01762
    2846 High confidence 0.00001 0.00001 1
    ctf18, chromosome transmission fidelity factor 18 homolog; homolog of yeast chl12. [refseq;acc:nm_022092] 1619 CHTF18 Low confidence 200.714 196.617 1.02084
    ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812] 1755 CTPS High confidence 180.609 178.393 1.01242
    4648 Low confidence 198.39 197.136 1.00636
    cug triplet repeat rna-binding protein 1 (cug-bp1) (rna-binding protein brunol-2) (deadenylation factor cug-bp) (50 kda nuclear polyadenylated rna-binding protein) (eden-bp). [swissprot;acc:q92879] 1801 CUGBP1 High confidence 217.984 215.441 1.0118
    3133 Low confidence 203.381 200.103 1.01638
    cug triplet repeat, rna binding protein 2; elav-type rna-binding protein; cug triplet repeat,rna-binding protein 2; cug triplet repeat, rna-binding protein 2; neuroblastoma apoptosis-related rna-binding protein. [refseq;acc:nm_006561] 1804 CUGBP2 High confidence 217.984 215.442 1.0118
    3166 Low confidence 203.392 200.152 1.01619
    cullin homolog 1 (cul-1). [swissprot;acc:q13616] 212 CUL1 High confidence 285.684 252.234 1.13261
    625 Low confidence 203.853 198.057 1.02926
    cullin homolog 2 (cul-2). [swissprot;acc:q13617] 210 CUL2 High confidence 285.684 252.234 1.13261
    642 Low confidence 203.883 198.148 1.02894
    cyclic-amp-dependent transcription factor atf-2 (activating transcription factor 2) (camp response element binding protein cre- bp1) (hb16). [swissprot;acc:p15336] 1401 ATF2 High confidence 218.657 214.11 1.02124
    2274 Low confidence 201.301 197.582 1.01882
    cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] 28 ATF3 High confidence 201.949 153.671 1.31416
    29 Low confidence 203.115 170.557 1.19089
    cyclic-amp-dependent transcription factor atf-6 alpha (activating transcription factor 6 alpha) (atf6-alpha). [swissprot;acc:p18850] 1683 ATF6 High confidence 216.899 213.889 1.01407
    1856 Low confidence 203.096 199.132 1.01991
    cyclic-amp-dependent transcription factor atf-6 beta (activating transcription factor 6 beta) (atf6-beta) (camp responsive element binding protein-like 1) (camp response element binding protein-related protein) (creb-rp) (g13 protein). [swissprot;acc:q99941] 1680 CREBL1 High confidence 216.899 213.889 1.01407
    1853 Low confidence 203.096 199.132 1.01991
    cyclic-amp-dependent transcription factor atf-7 (activating transcription factor 7) (transcription factor atf-a). [swissprot;acc:p17544] 1400 ATF7 High confidence 218.667 214.118 1.02125
    2226 Low confidence 201.046 197.31 1.01893
    cyclin a1. [swissprot;acc:p78396] 614 CCNA1 187.808 182.419 1.02954
    cyclin b3 isoform 1. [refseq;acc:nm_033670] 3215 CCNB3 202.049 198.87 1.01599
    cyclin c. [swissprot;acc:p24863] 1812 CCNC High confidence 217.071 214.564 1.01168
    4200 Low confidence 199.253 197.241 1.0102
    cyclin fold protein 1; cyclin-box carrying protein 1. [refseq;acc:nm_145012] 766 CCNY 206.437 201.034 1.02688
    cyclin g-associated kinase (ec 2.7.1.-). [swissprot;acc:o14976] 2074 GAK 201.829 198.007 1.0193
    cyclin g1 (cyclin g). [swissprot;acc:p51959] 963 CCNG1 High confidence 130.066 134.527 1.0343
    2485 Low confidence 202.785 199.153 1.01824
    cyclin g2. [swissprot;acc:q16589] 962 CCNG2 High confidence 130.066 134.527 1.0343
    2365 Low confidence 203.119 199.416 1.01857
    cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946] 1487 CCNH 201.236 197.009 1.02146
    2983 High confidence 0.00001 0.00001 1
    cyclin k. [swissprot;acc:o75909] 3160 CCNK
    4498 Low confidence 202.09 203.853 1.00872
    cyclin l1; cyclin l ania-6a. [refseq;acc:nm_020307] 4761 CCNL1 207.254 208.288 1.00499
    cyclin m1; ancient conserved domain protein 1. [refseq;acc:nm_020348] 2030 CNNM1 199.275 195.481 1.01941
    2606 High confidence 214.5 214.198 1.00141
    cyclin m2; ancient conserved domain protein 2. [refseq;acc:nm_017649] 2028 CNNM2 Low confidence 199.28 195.486 1.01941
    2604 High confidence 214.486 214.184 1.00141
    cyclin m3; ancient conserved domain protein 3. [refseq;acc:nm_017623] 2032 CNNM3 Low confidence 199.274 195.481 1.0194
    2601 High confidence 214.502 214.2 1.00141
    cyclin m4; ancient conserved domain protein 4. [refseq;acc:nm_020184] 2027 CNNM4 Low confidence 199.277 195.483 1.01941
    2603 High confidence 214.494 214.192 1.00141
    cyclin t1 (cyclin t) (cyct1). [swissprot;acc:o60563] 2619 CCNT1 Low confidence 202.506 206.117 1.01783
    3002 High confidence 0.00001 0.00001 1

    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/