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 808 to 857 of 3228 in total
    Network Comparison Type  : Divided
    Value Type  : Ranked
    Interaction Map  : High confidence
    Filtered  : 1
    description
    		Rank
    		Hugo
    		red
    		green
    		network_comparison
    dna excision repair protein ercc-1. [swissprot;acc:p07992] 3216 ERCC1 0.00001 0.00001 1
    dna fragmentation factor 40 kda subunit (ec 3.-.-.-) (dff-40) (caspase-activated deoxyribonuclease) (caspase-activated dnase) (cad) (caspase-activated nuclease) (cpan). [swissprot;acc:o76075] 2515 DFFB 215.835 216.341 1.00234
    dna fragmentation factor alpha subunit (dna fragmentation factor 45 kda subunit) (dff-45) (inhibitor of cad) (icad). [swissprot;acc:o00273] 2517 DFFA
    dna ligase i (ec 6.5.1.1) (polydeoxyribonucleotide synthase [atp]). [swissprot;acc:p18858] 3103 LIG1 0.00001 0.00001 1
    dna ligase iv (ec 6.5.1.1) (polydeoxyribonucleotide synthase [atp]). [swissprot;acc:p49917] 2808 LIG4
    dna methyltransferase 1-associated protein 1 (dnmt1-associated protein 1) (dnmap1). [swissprot;acc:q9npf5] 2796 DMAP1
    dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692] 1878 MLH1 212.186 214.467 1.01075
    dna mismatch repair protein mlh3 (mutl protein homolog 3). [swissprot;acc:q9uhc1] 1749 MLH3 206.058 203.485 1.01264
    dna mismatch repair protein msh2. [swissprot;acc:p43246] 3151 MSH2 0.00001 0.00001 1
    dna mismatch repair protein msh6 (muts-alpha 160 kda subunit) (g/t mismatch binding protein) (gtbp) (gtmbp) (p160). [swissprot;acc:p52701] 3045 MSH6
    dna polymerase delta p38 subunit. [refseq;acc:nm_015584] 1872 POLDIP2 222.819 225.228 1.01081
    dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] 176 POLE4 275.754 235.908 1.1689
    dna polymerase epsilon p17 subunit (dna polymerase epsilon subunit 3) (chromatin accessibility complex 17) (huchrac17) (chrac-17). [swissprot;acc:q9nrf9] 1447 POLE3 250.854 255.842 1.01988
    dna polymerase epsilon subunit b (ec 2.7.7.7) (dna polymerase ii subunit b). [swissprot;acc:p56282] 1615 POLE2 246.38 242.596 1.0156
    dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864] 694 POLE 241.907 229.35 1.05475
    dna polymerase gamma subunit 1 (ec 2.7.7.7) (mitochondrial dna polymerase catalytic subunit) (polg-alpha). [swissprot;acc:p54098] 2074 POLG 216.324 214.599 1.00804
    dna repair protein rad51 homolog 1 (hrad51) (hsrad51). [swissprot;acc:q06609] 2345 RAD51 219.878 218.893 1.0045
    dna repair protein rad52 homolog. [swissprot;acc:p43351] 404 RAD52 207.908 226.218 1.08807
    dna replication licensing factor mcm3 (dna polymerase alpha holoenzyme-associated protein p1) (rlf beta subunit) (p102 protein) (p1-mcm3). [swissprot;acc:p25205] 1891 MCM3 233.828 231.395 1.01051
    dna replication licensing factor mcm5 (cdc46 homolog) (p1-cdc46). [swissprot;acc:p33992] 1673 MCM5 228.496 231.729 1.01415
    dna replication licensing factor mcm8 (minichromosome maintenance 8). [swissprot;acc:q9uja3] 3011 MCM8 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
    dna topoisomerase ii, alpha isozyme (ec 5.99.1.3). [swissprot;acc:p11388] 1790 no value 203.759 201.349 1.01197
    dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880] 1796 TOP2B 201.357 1.01193
    dna topoisomerase iii alpha (ec 5.99.1.2). [swissprot;acc:q13472] 2015 TOP3A 217.941 215.979 1.00908
    dna-(apurinic or apyrimidinic site) lyase (ec 4.2.99.18) (ap endonuclease 1) (apex nuclease) (apen) (ref-1 protein). [swissprot;acc:p27695] 1840 APEX1 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] 2684 CSDA 208.438 208.635 1.00095
    dna-binding protein rfxank (regulatory factor x subunit b) (rfx-b) (ankyrin repeat family a protein 1). [swissprot;acc:o14593] 817 RFXANK 212.386 221.785 1.04425
    dna-directed rna polymerase i 135 kda polypeptide (ec 2.7.7.6) (rna polymerase i subunit 2) (rpa135). [swissprot;acc:q9h9y6] 416 POLR1B 240.6 261.041 1.08496
    dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0] 1071 no value 231.277 238.356 1.03061
    dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [swissprot;acc:o15160] 413 POLR1C 240.913 261.45 1.08525
    dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [swissprot;acc:o95602] 377 POLR1A 242.691 265.481 1.09391
    dna-directed rna polymerase ii 13.3 kda polypeptide (ec 2.7.7.6) (rpb11). [swissprot;acc:p52435] 896 POLR2J 230.811 239.785 1.03888
    dna-directed rna polymerase ii 14.4 kda polypeptide (ec 2.7.7.6) (rpb6) (rpb14.4) (rpabc2). [swissprot;acc:p41584] 780 POLR2F 232.762 243.933 1.04799
    dna-directed rna polymerase ii 14.5 kda polypeptide (ec 2.7.7.6) (rpb9) (rpb14.5). [swissprot;acc:p36954] 819 POLR2I 228.563 238.668 1.04421
    dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [swissprot;acc:p30876] 364 POLR2B 243.208 266.617 1.09625
    dna-directed rna polymerase ii 16 kda polypeptide (ec 2.7.7.6) (rpb4). [swissprot;acc:o15514] 688 POLR2D 237.554 250.823 1.05586
    dna-directed rna polymerase ii 19 kda polypeptide (ec 2.7.7.6) (rpb7). [swissprot;acc:p52433] 676 POLR2G 232.469 245.613 1.05654
    dna-directed rna polymerase ii 23 kda polypeptide (ec 2.7.7.6) (rpb25) (xap4) (rpb5) (rpabc1). [swissprot;acc:p19388] 427 POLR2E 239.977 259.525 1.08146
    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 240.287 260.193 1.08284
    dna-directed rna polymerase ii 7.6 kda polypeptide (ec 2.7.7.6) (rpb10) (rpb7.6) (rpabc5). [swissprot;acc:p52436] 538 POLR2L 237.627 253.604 1.06724
    dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928] 327 POLR2A 243.817 267.962 1.09903
    dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [swissprot;acc:o14802] 375 POLR3A 242.686 265.516 1.09407
    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 236.662 252.708 1.0678
    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 223.415 224.989 1.00705
    dna-directed rna polymerases iii 39 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c39 subunit). [swissprot;acc:q9h1d9] 463 POLR3F 238.921 257.327 1.07704
    dna-repair protein complementing xp-a cells (xeroderma pigmentosum group a complementing protein). [swissprot;acc:p23025] 2971 XPA 0.00001 0.00001 1
    dna-repair protein complementing xp-f cell (xeroderma pigmentosum group f complementing protein) (dna excision repair protein ercc-4). [swissprot;acc:q92889] 2801 ERCC4
    dna-repair protein complementing xp-g cells (xeroderma pigmentosum group g complementing protein) (dna excision repair protein ercc-5). [swissprot;acc:p28715] 950 ERCC5 252.873 261.821 1.03539
    dna-repair protein xrcc3 (x-ray repair cross-complementing protein 3). [swissprot;acc:o43542] 1702 XRCC3 216.079 219.024 1.01363

    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/