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 475 to 524 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    description
    		Rank
    		Hugo
    		red
    		green
    		network_comparison
    calcium/calmodulin-dependent protein kinase type ii alpha chain (ec 2.7.1.123) (cam-kinase ii alpha chain) (cam kinase ii alpha subunit) (camk-ii alpha subunit). [swissprot;acc:q9uqm7] 2172 CAMK2A 215.925 214.481 1.00673
    calcium/calmodulin-dependent protein kinase type ii beta chain (ec 2.7.1.123) (cam-kinase ii beta chain) (cam kinase ii beta subunit) (camk-ii beta subunit). [swissprot;acc:q13554] 2173 CAMK2B
    calcium/calmodulin-dependent protein kinase type ii delta chain (ec 2.7.1.123) (cam-kinase ii delta chain) (cam kinase ii delta subunit) (camk-ii delta subunit). [swissprot;acc:q13557] 2162 CAMK2D
    calcium/calmodulin-dependent protein kinase type ii gamma chain (ec 2.7.1.123) (cam-kinase ii gamma chain) (cam kinase ii gamma subunit) (camk-ii gamma subunit) (fragment). [swissprot;acc:q13555] 2161 CAMK2G
    calcyphosine. [swissprot;acc:q13938] 563 CAPS 220.744 207.121 1.06577
    calmegin precursor. [swissprot;acc:o14967] 1909 CLGN 217.48 215.256 1.01033
    calmodulin. [swissprot;acc:p02593] 2928 no value 0.00001 0.00001 1
    calnexin precursor (major histocompatibility complex class i antigen-binding protein p88) (p90) (ip90). [swissprot;acc:p27824] 1910 CANX 217.48 215.256 1.01033
    calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] 299 CAPN1 268.635 243.592 1.10281
    calpain 2, large [catalytic] subunit precursor (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (m-type) (m-calpain) (millimolar-calpain) (calpain large polypeptide l2). [swissprot;acc:p17655] 298 CAPN2 268.632 243.588
    calreticulin precursor (crp55) (calregulin) (hacbp) (erp60). [swissprot;acc:p27797] 2181 CALR 227.117 225.62 1.00664
    calsyntenin-1 precursor. [swissprot;acc:o94985] 2699 CLSTN1 188.435 188.31 1.00066
    calsyntenin-2 precursor. [swissprot;acc:q9h4d0] 2705 CLSTN2 188.457 188.334 1.00065
    calsyntenin-3 precursor. [swissprot;acc:q9bqt9] 2706 CLSTN3 188.459 188.336
    camp response element-binding protein cre-bpa. [refseq;acc:nm_004904] 1363 CREB5 218.591 213.899 1.02194
    camp responsive element binding protein-like 2. [refseq;acc:nm_001310] 3078 CREBL2 0.00001 0.00001 1
    camp-dependent protein kinase type i-alpha regulatory chain (tissue- specific extinguisher-1) (tse1). [swissprot;acc:p10644] 3089 PRKAR1A
    camp-dependent protein kinase type ii-alpha regulatory chain. [swissprot;acc:p13861] 2307 PRKAR2A 215.554 214.467 1.00507
    camp-dependent protein kinase type ii-beta regulatory chain. [swissprot;acc:p31323] 2313 PRKAR2B 215.529 214.449 1.00504
    camp-dependent protein kinase, alpha-catalytic subunit (ec 2.7.1.37) (pka c-alpha). [swissprot;acc:p17612] 2312 PRKACA 215.542 214.459 1.00505
    camp-dependent protein kinase, beta-catalytic subunit (ec 2.7.1.37) (pka c-beta). [swissprot;acc:p22694] 2311 PRKACB
    camp-dependent protein kinase, gamma-catalytic subunit (ec 2.7.1.37) (pka c-gamma). [swissprot;acc:p22612] 2309 PRKACG
    candidate tumor suppressor in ovarian cancer 2. [refseq;acc:nm_080822] 1173 DPH1 229.243 235.246 1.02619
    carboxypeptidase a1 precursor (ec 3.4.17.1). [swissprot;acc:p15085] 1422 CPA1 203.979 208.229 1.02084
    carboxypeptidase a5. [refseq;acc:nm_080385] 1417 CPA5
    carboxypeptidase b precursor (ec 3.4.17.2) (pancreas-specific protein) (pasp). [swissprot;acc:p15086] 1418 CPB1
    carboxypeptidase b precursor. [refseq;acc:nm_020361] 509 CPA6 177.698 190.239 1.07057
    carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870] 717 CPE 223.121 211.685 1.05402
    carboxypeptidase n catalytic chain precursor (ec 3.4.17.3) (arginine carboxypeptidase) (kininase 1) (serum carboxypeptidase n) (scpn) (anaphylatoxin inactivator) (plasma carboxypeptidase b). [swissprot;acc:p15169] 715 CPN1
    carcinoma related gene. [refseq;acc:nm_016041] 3179 DERL2 0.00001 0.00001 1
    carnitine o-acetyltransferase (ec 2.3.1.7) (carnitine acetylase) (cat). [swissprot;acc:p43155] 1698 CRAT 217.624 214.69 1.01367
    carnitine o-palmitoyltransferase ii, mitochondrial precursor (ec 2.3.1.21) (cpt ii). [swissprot;acc:p23786] 2885 CPT2 0.00001 0.00001 1
    cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] 226 COMP 239.991 269.238 1.12187
    casein kinase i alpha s-like. [refseq;acc:nm_145203] 1495 CSNK1A1L 229.459 225.237 1.01874
    casein kinase i, alpha isoform (ec 2.7.1.-) (cki-alpha) (ck1). [swissprot;acc:p48729] 1496 CSNK1A1
    casein kinase i, delta isoform (ec 2.7.1.-) (cki-delta) (ckid). [swissprot;acc:p48730] 1721 CSNK1D 227.125 224.164 1.01321
    casein kinase i, epsilon isoform (ec 2.7.1.-) (cki-epsilon) (ckie). [swissprot;acc:p49674] 1710 no value 227.225 224.21 1.01345
    casein kinase i, gamma 1 isoform (ec 2.7.1.-) (cki-gamma 1). [swissprot;acc:q9hcp0] 2830 CSNK1G1 0.00001 0.00001 1
    casein kinase i, gamma 2 isoform (ec 2.7.1.-) (cki-gamma 2). [swissprot;acc:p78368] 2986 CSNK1G2
    casein kinase i, gamma 3 isoform (ec 2.7.1.-) (cki-gamma 3). [swissprot;acc:q9y6m4] 2901 CSNK1G3
    casein kinase ii beta chain (ck ii) (phosvitin) (g5a). [swissprot;acc:p13862] 936 no value 232.473 224.372 1.03611
    casein kinase ii, alpha chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19138] 863 CSNK2A1P 240.194 230.957 1.03999
    casein kinase ii, alpha' chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19784] 864 CSNK2A2
    caspase-7 precursor (ec 3.4.22.-) (ice-like apoptotic protease 3) (ice-lap3) (apoptotic protease mch-3) (cmh-1). [swissprot;acc:p55210] 1292 CASP7 233.942 228.46 1.024
    catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [refseq;acc:nm_003798] 1834 CTNNAL1 180.409 182.459 1.01136
    cathepsin b precursor (ec 3.4.22.1) (cathepsin b1) (app secretase). [swissprot;acc:p07858] 1667 CTSB 214.898 211.898 1.01416
    cathepsin l precursor (ec 3.4.22.15) (major excreted protein) (mep). [swissprot;acc:p07711] 1426 CTSL1 214.717 219.157 1.02068
    cathepsin l2 precursor (ec 3.4.22.43) (cathepsin v) (cathepsin u). [swissprot;acc:o60911] 1425 CTSL2
    caveolin-1. [swissprot;acc:q03135] 3099 CAV1 0.00001 0.00001 1
    caveolin-3 (m-caveolin). [swissprot;acc:p56539] 2779 CAV3

    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/