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 [...,...].
    Rank Gene Hugo description Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2851 to 2900 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Network Comparison Type
    		Value Type
    		red
    		green
    		network_comparison
    357 CHMP4A protein hspc134 (protein cda04). [swissprot;acc:q9by43] Subtracted Ranked 94 114 20
    DVL1 segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] Measured 4977.09 5966.44 989.35
    GRB2 growth factor receptor-bound protein 2 (grb2 adapter protein) (sh2/sh3 adapter grb2) (ash protein). [swissprot;acc:p29354] Divided Rooted 61.2684 67.755 1.10587
    IMMP2L imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549] Measured 5061.11 5950.22 1.17567
    PPP2R2D uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] Squared 9811.86 7908.29 1.24071
    PRKAB1 5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478] Subtracted 34129.6 40434.5 6304.9
    358 no value microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378] Divided Measured 5061.11 5950.22 1.17567
    serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [swissprot;acc:q00007] Squared 9811.73 7908.13 1.24071
    DVL2 segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] Subtracted Measured 4977.8 5966.14 988.34
    NEK2 serine/threonine-protein kinase nek2 (ec 2.7.1.37) (nima-related protein kinase 2) (nima-like protein kinase 1) (hspk 21). [swissprot;acc:p51955] Divided Rooted 61.2684 67.755 1.10587
    NFYB nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [swissprot;acc:p25208] Subtracted 51.6736 58.4422 6.7686
    PRKAG2 5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0] Squared 34129.6 40434.5 6304.9
    RAB37 ras-related protein rab-37. [swissprot;acc:q96ax2] Ranked 240.287 260.193 19.906
    RPL10L ribosomal protein l10-like protein. [refseq;acc:nm_080746] Divided 243.12 266.662 1.09683
    359 CDK3 cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] Measured 12798.9 10887.2 1.17559
    NDUFS4 nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181] Subtracted 1920.75 2907.43 986.68
    PES1 pescadillo homolog 1. [swissprot;acc:o00541] Divided Rooted 49.2488 54.4603 1.10582
    PPP2R2B serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [swissprot;acc:q00005] Squared 9812.34 7908.87 1.24068
    PRKAA1 5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131] Subtracted 34129.4 40434.2 6304.8
    RAB26 ras-related protein rab-26. [swissprot;acc:q9ulw5] Ranked 240.287 260.193 19.906
    RPL4 60s ribosomal protein l4 (l1). [swissprot;acc:p36578] Divided 239.277 262.434 1.09678
    SART1 squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [refseq;acc:nm_005146] Subtracted Rooted 57.6823 64.4212 6.7389
    360 CCNB2 g2/mitotic-specific cyclin b2. [swissprot;acc:o95067] Divided Measured 12796.8 10886 1.17553
    DDX24 atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7] Subtracted Rooted 46.901 53.624 6.723
    GNL3 nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366] Divided 49.3771 54.5905 1.10558
    LSM8 u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] Subtracted Measured 4590.18 5575.52 985.34
    POLR2C dna-directed rna polymerase ii 33 kda polypeptide (ec 2.7.7.6) (rpb3) (rna polymerase ii subunit 3) (rpb33) (rpb31). [swissprot;acc:p19387] Ranked 240.287 260.193 19.906
    PPP2R2C serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [swissprot;acc:q9y2t4] Divided Squared 9814.47 7911.48 1.24054
    SEC61G protein transport protein sec61 gamma subunit. [swissprot;acc:p38384] Ranked 243.072 266.559 1.09663
    VAV2 vav-2 protein. [swissprot;acc:p52735] Subtracted Squared 31377.3 37670.1 6292.8
    361 CAPN2 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] Rooted 46.8525 53.5324 6.6799
    CBL cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681] Measured 6875.08 7858.38 983.3
    CDK2 cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941] Divided 12787.6 10880.5 1.17528
    KATNA1 katanin p60 subunit a 1. [refseq;acc:nm_007044] Subtracted Ranked 232.431 252.238 19.807
    MRPL17 mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061] Divided 242.83 266.248 1.09644
    RPS4Y2 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] Rooted 50.7801 45.9472 1.10518
    SFPQ splicing factor, proline-and glutamine-rich (polypyrimidine tract- binding protein-associated splicing factor) (ptb-associated splicing factor) (psf) (dna-binding p52/p100 complex, 100 kda subunit). [swissprot;acc:p23246] Squared 70694.1 56989.9 1.24047
    TPT1 translationally controlled tumor protein (tctp) (p23) (histamine- releasing factor) (hrf). [swissprot;acc:p13693] Subtracted 42363.8 36083.8 6280
    362 no value 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] Divided Rooted 50.7803 45.9477 1.10518
    nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594] Subtracted Squared 34071.5 40336.5 6265
    CAPN1 calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] Rooted 46.8525 53.5316 6.6791
    CCNB1 g2/mitotic-specific cyclin b1. [swissprot;acc:p14635] Divided Measured 12786.6 10879.9 1.17525
    DVL3 segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] Subtracted 4981.52 5964.58 983.06
    KATNB1 katanin p80 subunit b 1; katanin (80 kda); katanin p80 (wd40-containing) subunit b 1. [refseq;acc:nm_005886] Ranked 232.382 252.166 19.784
    SHROOM2 apical-like protein (apxl protein). [swissprot;acc:q13796] Divided 231.492 211.136 1.09641
    TAF7 transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545] Squared 57808.9 46630.3 1.23973
    363 no value alpha-nac protein. [sptrembl;acc:q9h009] Subtracted 34069.4 40333 6263.6
    BOP1 block of proliferation 1. [swissprot;acc:q14137] Divided Rooted 49.4884 54.6735 1.10477
    CBLB signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191] Subtracted Measured 6856.71 7838.3 981.59
    CDC2 cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493] Divided 12780.7 10876.4 1.17509

    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/