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 2058 to 2107 of 8289 in total
    Network Comparison Type  : Divided
    Value Type  : Ranked
    Filtered  : 1
    description
    		Rank
    		Hugo
    		Interaction Map
    		red
    		green
    		network_comparison
    dna topoisomerase i (ec 5.99.1.2). [swissprot;acc:p11387] 2166 no value Low confidence 202.946 199.148 1.01907
    dna topoisomerase i, mitochondrial precursor (ec 5.99.1.2) (top1mt). [swissprot;acc:q969p6] 2175 TOP1MT 202.944 199.153 1.01904
    dna topoisomerase ii, alpha isozyme (ec 5.99.1.3). [swissprot;acc:p11388] 1240 no value 201.458 196.99 1.02268
    1790 High confidence 203.759 201.349 1.01197
    dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880] 1241 TOP2B Low confidence 201.449 196.981 1.02268
    1796 High confidence 203.759 201.357 1.01193
    dna topoisomerase iii alpha (ec 5.99.1.2). [swissprot;acc:q13472] 2015 TOP3A 217.941 215.979 1.00908
    2425 Low confidence 201.085 197.448 1.01842
    dna-(apurinic or apyrimidinic site) lyase (ec 4.2.99.18) (ap endonuclease 1) (apex nuclease) (apen) (ref-1 protein). [swissprot;acc:p27695] 1518 APEX1 200.093 195.912 1.02134
    1840 High confidence 211.882 209.544 1.01116
    dna-binding protein a (cold shock domain protein a) (single-strand dna binding protein nf-gmb). [swissprot;acc:p16989] 1144 CSDA Low confidence 203.991 199.319 1.02344
    2684 High confidence 208.438 208.635 1.00095
    dna-binding protein rfx2. [swissprot;acc:p48378] 3913 RFX2 Low confidence 203.974 201.439 1.01258
    dna-binding protein rfxank (regulatory factor x subunit b) (rfx-b) (ankyrin repeat family a protein 1). [swissprot;acc:o14593] 817 RFXANK High confidence 212.386 221.785 1.04425
    4196 Low confidence 203.591 201.529 1.01023
    dna-crosslink repair gene snm1. [refseq;acc:nm_014881] 1062 no value 203.048 198.295 1.02397
    dna-directed rna polymerase i 135 kda polypeptide (ec 2.7.7.6) (rna polymerase i subunit 2) (rpa135). [swissprot;acc:q9h9y6] 416 POLR1B High confidence 240.6 261.041 1.08496
    3720 Low confidence 201.796 199.085 1.01362
    dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0] 1071 no value High confidence 231.277 238.356 1.03061
    1801 Low confidence 196.761 192.879 1.02013
    dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [swissprot;acc:o15160] 413 POLR1C High confidence 240.913 261.45 1.08525
    4683 Low confidence 203.603 202.427 1.00581
    dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [swissprot;acc:o95602] 377 POLR1A High confidence 242.691 265.481 1.09391
    4035 Low confidence 203.128 200.822 1.01148
    dna-directed rna polymerase ii 13.3 kda polypeptide (ec 2.7.7.6) (rpb11). [swissprot;acc:p52435] 896 POLR2J High confidence 230.811 239.785 1.03888
    4968 Low confidence 201.324 201.507 1.00091
    dna-directed rna polymerase ii 14.4 kda polypeptide (ec 2.7.7.6) (rpb6) (rpb14.4) (rpabc2). [swissprot;acc:p41584] 780 POLR2F High confidence 232.762 243.933 1.04799
    3353 Low confidence 202.26 199.165 1.01554
    dna-directed rna polymerase ii 14.5 kda polypeptide (ec 2.7.7.6) (rpb9) (rpb14.5). [swissprot;acc:p36954] 819 POLR2I High confidence 228.563 238.668 1.04421
    2105 Low confidence 200.982 197.188 1.01924
    dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [swissprot;acc:p30876] 364 POLR2B High confidence 243.208 266.617 1.09625
    4588 Low confidence 204.291 202.806 1.00732
    dna-directed rna polymerase ii 16 kda polypeptide (ec 2.7.7.6) (rpb4). [swissprot;acc:o15514] 688 POLR2D High confidence 237.554 250.823 1.05586
    3351 Low confidence 204.204 201.079 1.01554
    dna-directed rna polymerase ii 19 kda polypeptide (ec 2.7.7.6) (rpb7). [swissprot;acc:p52433] 676 POLR2G High confidence 232.469 245.613 1.05654
    4118 Low confidence 202.818 200.679 1.01066
    dna-directed rna polymerase ii 23 kda polypeptide (ec 2.7.7.6) (rpb25) (xap4) (rpb5) (rpabc1). [swissprot;acc:p19388] 427 POLR2E High confidence 239.977 259.525 1.08146
    3270 Low confidence 201.848 198.721 1.01574
    dna-directed rna polymerase ii 33 kda polypeptide (ec 2.7.7.6) (rpb3) (rna polymerase ii subunit 3) (rpb33) (rpb31). [swissprot;acc:p19387] 424 POLR2C High confidence 240.287 260.193 1.08284
    4584 Low confidence 205.627 204.099 1.00749
    dna-directed rna polymerase ii 7.6 kda polypeptide (ec 2.7.7.6) (rpb10) (rpb7.6) (rpabc5). [swissprot;acc:p52436] 538 POLR2L High confidence 237.627 253.604 1.06724
    3871 Low confidence 202.466 199.89 1.01289
    dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928] 327 POLR2A High confidence 243.817 267.962 1.09903
    4616 Low confidence 204.378 202.986 1.00686
    dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [swissprot;acc:o14802] 375 POLR3A High confidence 242.686 265.516 1.09407
    3191 Low confidence 204.624 201.384 1.01609
    dna-directed rna polymerases i, ii, and iii 17.1 kda polypeptide (ec 2.7.7.6) (rpb17) (rpb8) (rpabc3). [swissprot;acc:p52434] 535 POLR2H High confidence 236.662 252.708 1.0678
    3674 Low confidence 202.287 199.519 1.01387
    dna-directed rna polymerases iii 12.5 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c11 subunit) (hsc11p) (hrpc11) (my010 protein). [swissprot;acc:q9y2y1] 2112 POLR3K High confidence 223.415 224.989 1.00705
    2971 Low confidence 202.057 198.709 1.01685

    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/