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 2025 to 2074 of 8289 in total
    Network Comparison Type  : Divided
    Value Type  : Ranked
    Filtered  : 1
    description
    		Rank
    		Hugo
    		Interaction Map
    		red
    		green
    		network_comparison
    dna polymerase alpha catalytic subunit (ec 2.7.7.7). [swissprot;acc:p09884] 2859 POLA1 Low confidence 200.659 197.277 1.01714
    dna polymerase delta catalytic subunit (ec 2.7.7.7) (dna polymerase delta subunit p125). [swissprot;acc:p28340] 2372 POLD1 197.53 193.931 1.01856
    dna polymerase delta p38 subunit. [refseq;acc:nm_015584] 753 POLDIP2 202.039 196.717 1.02705
    1872 High confidence 222.819 225.228 1.01081
    dna polymerase delta subunit 2 (ec 2.7.7.7). [swissprot;acc:p49005] 2369 POLD2 Low confidence 197.53 193.931 1.01856
    dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] 176 POLE4 High confidence 275.754 235.908 1.1689
    386 Low confidence 205.821 198.494 1.03691
    dna polymerase epsilon p17 subunit (dna polymerase epsilon subunit 3) (chromatin accessibility complex 17) (huchrac17) (chrac-17). [swissprot;acc:q9nrf9] 1447 POLE3 High confidence 250.854 255.842 1.01988
    1606 Low confidence 204.475 200.292 1.02088
    dna polymerase epsilon subunit b (ec 2.7.7.7) (dna polymerase ii subunit b). [swissprot;acc:p56282] 1615 POLE2 High confidence 246.38 242.596 1.0156
    2285 Low confidence 200.812 197.109 1.01879
    dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864] 694 POLE High confidence 241.907 229.35 1.05475
    720 Low confidence 204.279 198.814 1.02749
    dna polymerase gamma subunit 1 (ec 2.7.7.7) (mitochondrial dna polymerase catalytic subunit) (polg-alpha). [swissprot;acc:p54098] 905 POLG 201.688 196.714 1.02529
    2074 High confidence 216.324 214.599 1.00804
    dna polymerase zeta catalytic subunit (ec 2.7.7.7) (hrev3). [swissprot;acc:o60673] 3624 REV3L Low confidence 200.681 197.868 1.01422
    dna repair protein rad51 homolog 1 (hrad51) (hsrad51). [swissprot;acc:q06609] 1232 RAD51 200.818 196.355 1.02273
    2345 High confidence 219.878 218.893 1.0045
    dna repair protein rad52 homolog. [swissprot;acc:p43351] 404 RAD52 207.908 226.218 1.08807
    1201 Low confidence 203.852 199.266 1.02301
    dna replication factor; double parked, drosophila, homolog of. [refseq;acc:nm_030928] 707 CDT1 204.969 199.442 1.02771
    dna replication licensing factor mcm2 (nuclear protein bm28). [swissprot;acc:p49736] 1194 MCM2 202.182 197.621 1.02308
    dna replication licensing factor mcm3 (dna polymerase alpha holoenzyme-associated protein p1) (rlf beta subunit) (p102 protein) (p1-mcm3). [swissprot;acc:p25205] 1131 MCM3 202.3 197.652 1.02352
    1891 High confidence 233.828 231.395 1.01051
    dna replication licensing factor mcm4 (cdc21 homolog) (p1-cdc21). [swissprot;acc:p33991] 1734 MCM4 Low confidence 201.225 197.196 1.02043
    dna replication licensing factor mcm5 (cdc46 homolog) (p1-cdc46). [swissprot;acc:p33992] 1248 MCM5 202.294 197.813 1.02265
    1673 High confidence 228.496 231.729 1.01415
    dna replication licensing factor mcm6 (p105mcm). [swissprot;acc:q14566] 1333 MCM6 Low confidence 202.379 197.993 1.02215
    dna replication licensing factor mcm7 (cdc47 homolog) (p1.1-mcm3). [swissprot;acc:p33993] 1146 MCM7 201.363 196.754 1.02343
    dna replication licensing factor mcm8 (minichromosome maintenance 8). [swissprot;acc:q9uja3] 2776 MCM8 202.549 199.082 1.01741
    3011 High confidence 0.00001 0.00001 1
    dna segment on chromosome 6(unique) 2654 expressed sequence; dna segment on chromosome x (unique) 2654 expressed sequence. [refseq;acc:nm_012135] 1681 FAM50B 216.899 213.889 1.01407
    1855 Low confidence 203.096 199.132 1.01991
    dna topoisomerase i (ec 5.99.1.2). [swissprot;acc:p11387] 2166 no value 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

    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/