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 Gene Rank Network Comparison Type Hugo Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2151 to 2200 of 3228 in total
    Network Comparison Type  : Divided
    Value Type  : Ranked
    Interaction Map  : High confidence
    Filtered  : 1
    description
    		Rank
    		Hugo
    		red
    		green
    		network_comparison
    proteasome subunit alpha type 7 (ec 3.4.25.1) (proteasome subunit rc6-1) (proteasome subunit xapc7). [swissprot;acc:o14818] 2280 PSMA7 212.793 211.657 1.00537
    proteasome subunit alpha type 7-like (ec 3.4.25.1). [swissprot;acc:q8taa3] 2283 PSMA8 212.81 211.676 1.00536
    proteasome subunit beta type 1 (ec 3.4.25.1) (proteasome component c5) (macropain subunit c5) (multicatalytic endopeptidase complex subunit c5) (proteasome gamma chain). [swissprot;acc:p20618] 2324 PSMB1 212.129 211.129 1.00474
    proteasome subunit beta type 10 precursor (ec 3.4.25.1) (proteasome mecl-1) (macropain subunit mecl-1) (multicatalytic endopeptidase complex subunit mecl-1). [swissprot;acc:p40306] 2009 CTRL 216.201 214.245 1.00913
    proteasome subunit beta type 2 (ec 3.4.25.1) (proteasome component c7-i) (macropain subunit c7-i) (multicatalytic endopeptidase complex subunit c7-i). [swissprot;acc:p49721] 2612 PSMB2 215.497 215.799 1.0014
    proteasome subunit beta type 3 (ec 3.4.25.1) (proteasome theta chain) (proteasome chain 13) (proteasome component c10-ii). [swissprot;acc:p49720] 2407 PSMB3 214.234 213.456 1.00364
    proteasome subunit beta type 4 precursor (ec 3.4.25.1) (proteasome beta chain) (macropain beta chain) (multicatalytic endopeptidase complex beta chain) (proteasome chain 3) (hsn3) (hsbpros26). [swissprot;acc:p28070] 1641 PSMB4 218.167 215.034 1.01457
    proteasome subunit beta type 5 precursor (ec 3.4.25.1) (proteasome epsilon chain) (macropain epsilon chain) (multicatalytic endopeptidase complex epsilon chain) (proteasome subunit x) (proteasome chain 6) (proteasome subunit mb1). [swissprot;acc:p28074] 2387 PSMB5 211.301 210.475 1.00392
    proteasome subunit beta type 6 precursor (ec 3.4.25.1) (proteasome delta chain) (macropain delta chain) (multicatalytic endopeptidase complex delta chain) (proteasome subunit y). [swissprot;acc:p28072] 2450 PSMB6 213.85 213.177 1.00316
    proteasome subunit beta type 7 precursor (ec 3.4.25.1) (proteasome subunit z) (macropain chain z) (multicatalytic endopeptidase complex chain z). [swissprot;acc:q99436] 2686 PSMB7 219.829 219.629 1.00091
    proteasome subunit beta type 8 precursor (ec 3.4.25.1) (proteasome component c13) (macropain subunit c13) (multicatalytic endopeptidase complex subunit c13). [swissprot;acc:p28062] 2530 no value 212.464 211.99 1.00224
    proteasome subunit beta type 9 precursor (ec 3.4.25.1) (proteasome chain 7) (macropain chain 7) (multicatalytic endopeptidase complex chain 7) (ring12 protein) (low molecular mass protein 2). [swissprot;acc:p28065] 2545 213.494 213.088 1.00191
    protein 1-4 (atp binding protein associated with cell differentiation). [swissprot;acc:o14530] 352 TXNDC9 242.14 265.696 1.09728
    protein 4.1 (band 4.1) (p4.1) (epb4.1) (4.1r). [swissprot;acc:p11171] 2142 EPB41 206.443 207.864 1.00688
    protein ad-016 (protein cgi-116) (x0009). [swissprot;acc:q9y3c0] 1505 CCDC53 216.158 212.316 1.0181
    protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] 188 PRMT1 226.582 198.444 1.14179
    protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678] 343 PRMT3 241.625 265.136 1.0973
    protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] 189 PRMT8 226.582 198.444 1.14179
    protein bap28. [swissprot;acc:q9h583] 1013 HEATR1 244.312 236.647 1.03239
    protein c14orf122 (cgi-112). [swissprot;acc:q9y3b6] 1819 C14orf122 220.462 217.926 1.01164
    protein c20orf24 (rab5-interacting protein) (rip5) (pnas-11). [swissprot;acc:q9buv8] 3131 C20orf24 0.00001 0.00001 1
    protein c20orf4 (protein cgi-23) (pro0225). [swissprot;acc:q9y312] 1587 C20orf4 220.129 216.598 1.0163
    protein c20orf43 (hspc164/hspc169) (ad-007) (cda05). [swissprot;acc:q9by42] 3206 C20orf43 0.00001 0.00001 1
    protein c20orf45 (cgi-107). [swissprot;acc:q9y3b1] 1570 SLMO2 221.128 224.767 1.01646
    protein c21orf2 (c21orf-humf09g8.5) (yf5/a2). [swissprot;acc:o43822] 2874 C21orf2 0.00001 0.00001 1
    protein c6orf55 (dopamine responsive protein drg-1) (my012 protein) (hspc228). [swissprot;acc:q9np79] 3219 VTA1
    protein cdc27hs (cell division cycle protein 27 homolog) (h-nuc). [swissprot;acc:p30260] 1357 CDC27 228.409 223.475 1.02208
    protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] 13 UFC1 288.754 212.554 1.3585
    protein cgi-140 (protein ptd008) (my006 protein). [swissprot;acc:q9y284] 3102 C19orf56 0.00001 0.00001 1
    protein cgi-147. [swissprot;acc:q9y3e5] 1490 PTRH2 221.961 226.186 1.01903
    protein cgi-27 (c21orf19-like protein). [swissprot;acc:q9y316] 539 MEMO1P 236.964 252.86 1.06708
    protein disulfide isomerase precursor (pdi) (ec 5.3.4.1) (prolyl 4- hydroxylase beta subunit) (cellular thyroid hormone binding protein) (p55). [swissprot;acc:p07237] 2188 P4HB 209.54 208.162 1.00662
    protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] 45 FOSB 204.641 161.051 1.27066
    protein hspc134 (protein cda04). [swissprot;acc:q9by43] 130 CHMP4A 94 114 1.21277
    protein kinase c and casein kinase substrate in neurons protein 1. [swissprot;acc:q9by11] 3020 PACSIN1 0.00001 0.00001 1
    protein kinase c and casein kinase substrate in neurons protein 2. [swissprot;acc:q9unf0] 3142 PACSIN2
    protein kinase c and casein kinase substrate in neurons protein 3 (sh3 domain-containing protein 6511) (endophilin i). [swissprot;acc:q9uks6] 2845 PACSIN3
    protein kinase c binding protein 1 (rack7) (cutaneous t-cell lymphoma associated antigen se14-3) (ctcl tumor antigen se14-3) (zinc finger mynd domain containing protein 8). [swissprot;acc:q9ulu4] 2501 ZMYND8 217.398 216.809 1.00272
    protein kinase c, delta type (ec 2.7.1.-) (npkc-delta). [swissprot;acc:q05655] 2857 PRKCD 0.00001 0.00001 1
    protein kinase c, epsilon type (ec 2.7.1.-) (npkc-epsilon). [swissprot;acc:q02156] 2399 PRKCE 182.4 183.083 1.00374
    protein kinase c, eta type (ec 2.7.1.-) (npkc-eta) (pkc-l). [swissprot;acc:p24723] 2398 PRKCH 182.395 183.079 1.00375
    protein kinase c, iota type (ec 2.7.1.37) (npkc-iota) (atypical protein kinase c-lamda/iota) (apkc-lambda/iota). [swissprot;acc:p41743] 967 PRKCI 211.987 204.964 1.03426
    protein kinase c, theta type (ec 2.7.1.-) (npkc-theta). [swissprot;acc:q04759] 3186 PRKCQ 0.00001 0.00001 1
    protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [swissprot;acc:q05513] 975 PRKCZ 211.987 204.964 1.03426
    protein kinase clk2 (ec 2.7.1.-) (cdc-like kinase 2). [swissprot;acc:p49760] 1604 CLK2 214.984 211.614 1.01593
    protein kinase clk3 (ec 2.7.1.-) (cdc-like kinase 3). [swissprot;acc:p49761] 1607 CLK3 214.982 211.622 1.01588
    protein kinase nyd-sp25. [refseq;acc:nm_033516] 1868 TPD52L3 207.642 209.895 1.01085
    protein kinase pkx1 (ec 2.7.1.-). [swissprot;acc:p51817] 2308 PRKX 215.543 214.459 1.00505
    protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] 55 PRKRAP1 320.927 254.434 1.26134
    protein phosphatase 1, regulatory (inhibitor) subunit 12a; myosin phosphatase, target subunit 1. [refseq;acc:nm_002480] 2014 PPP1R12A 217.676 215.709 1.00912

    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/