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 Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 825 to 874 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    description
    		Rank
    		Hugo
    		red
    		green
    		network_comparison
    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
    dnaj homolog subfamily b member 1 (heat shock 40 kda protein 1) (heat shock protein 40) (hsp40) (dnaj protein homolog 1) (hdj-1). [swissprot;acc:p25685] 771 DNAJB1 210.946 221.225 1.04873
    dnaj homolog subfamily b member 11 precursor (er-associated dnaj protein 3) (erj3) (er-associated hsp40 co-chaperone) (hdj9) (pwp1- interacting protein 4). [swissprot;acc:q9ubs4] 575 DNAJB11 221.807 208.264 1.06503
    dnaj homolog subfamily b member 4 (heat shock 40 kda protein 1 homolog) (heat shock protein 40 homolog) (hsp40 homolog). [swissprot;acc:q9udy4] 768 DNAJB4 210.946 221.225 1.04873
    dnaj homolog subfamily b member 5 (heat shock protein hsp40-3) (heat shock protein cognate 40) (hsc40) (hsp40-2). [swissprot;acc:o75953] 770 DNAJB5
    doc-1 related protein (doc-1r). [swissprot;acc:o75956] 331 CDK2AP2 312 284 1.09859
    docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704] 655 DOK1 216.504 204.622 1.05807
    docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496] 654 DOK2
    dok-like protein. [refseq;acc:nm_024872] 653 no value
    dolichol-phosphate mannosyltransferase (ec 2.4.1.83) (dolichol- phosphate mannose synthase) (dolichyl-phosphate beta-d- mannosyltransferase) (mannose-p-dolichol synthase) (mpd synthase) (dpm synthase). [swissprot;acc:o60762] 991 DPM1 203.381 196.76 1.03365
    dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656] 257 DDOST 200.691 179.88 1.11569
    dopachrome tautomerase precursor (ec 5.3.3.12) (dt) (dct) (dopachrome delta-isomerase) (tyrosinase-related protein 2) (trp-2) (trp2). [swissprot;acc:p40126] 1020 DCT 221.28 214.409 1.03205
    double-strand break repair protein mre11a (mre11 homolog 1). [swissprot;acc:p49959] 1046 MRE11A 173.475 178.889 1.03121
    double-stranded rna-binding zinc finger protein jaz. [refseq;acc:nm_012279] 3054 ZNF346 0.00001 0.00001 1
    doublecortin (lissencephalin-x) (lis-x) (doublin). [swissprot;acc:o43602] 2725 DCX 216.496 216.569 1.00034
    doublesex and mab-3 related transcription factor 3; testis-specific protein; dmrt-like family a3. [refseq;acc:nm_021240] 3187 DMRT3 0.00001 0.00001 1
    down-regulated in metastasis. [refseq;acc:nm_014503] 787 UTP20 244.447 233.508 1.04685
    dpy-30-like protein. [swissprot;acc:q9c005] 1815 no value 220.462 217.926 1.01164

    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/