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 description Gene Hugo Value Type Network Comparison Type red Interaction Map Filtered network_comparison green
    Results: HTML CSV LaTeX Showing element 580 to 629 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Value Type
    		Network Comparison Type
    		red
    		network_comparison
    		green
    73 melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1] MAGED2 Squared Divided 219048 1.68808 129762
    neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] NEUROD1 Rooted 27.9136 1.33581 37.2872
    nuclear inhibitor of protein phosphatase-1 (nipp-1) (protein phosphatase 1, regulatory inhibitor subunit 8) [includes: activator of rna decay (ec 3.1.4.-) (ard-1)]. [swissprot;acc:q12972] PPP1R8 Squared Subtracted 148058 48429.6 99628.4
    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] PPP2R2B Measured Divided 4556.83 1.54711 2945.38
    serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] PPP1CC Subtracted 22268.8 3708.4 18560.4
    74 a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] ARAF Squared 117858 47287.9 70570.1
    homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] no value Measured 20446.1 3690.3 24136.4
    junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] JPH2 Ranked Divided 288 1.25694 362
    neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] NEUROD4 Rooted 27.9136 1.33581 37.2872
    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] PPP2R2C Measured 4556.99 1.54694 2945.8
    serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [swissprot;acc:p30153] PPP2R1A Ranked Subtracted 189.07 53.383 242.453
    t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492] PBK Rooted 27.7254 16.3045 44.0299
    trophinin. [swissprot;acc:q12816] TRO Squared Divided 219048 1.68808 129762
    75 chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] CHD5 Rooted 27.9136 1.33581 37.2872
    homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] HOXB4 Measured Subtracted 20446.1 3690.3 24136.4
    kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] KHDRBS3 Rooted 27.7254 16.3045 44.0299
    myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] MYO5B Squared Divided 110342 1.67024 184298
    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] NDUFS4 Measured 1920.75 1.5137 2907.43
    raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] RAF1 Squared Subtracted 117850 47283.2 70566.8
    sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906] SMPD2 Ranked Divided 288 1.25694 362
    voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5] CACNG8 Subtracted 254.693 52.025 202.668
    76 cyclin g1 (cyclin g). [swissprot;acc:p51959] CCNG1 Squared 117718 47212.2 70505.8
    cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519] CDK2AP1 Rooted Divided 27.9136 1.33581 37.2872
    db83 protein. [swissprot;acc:p57088] TMEM33 Ranked 288 1.25694 362
    homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] HOXC5 Measured Subtracted 20446.1 3690.3 24136.4
    kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] KHDRBS1 Rooted 27.7254 16.3045 44.0299
    myosin vc (myosin 5c). [swissprot;acc:q9nqx4] MYO5C Squared Divided 110342 1.67024 184298
    serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, beta isoform (pp2a, subunit a, pr65-beta isoform) (pp2a, subunit a, r1-beta isoform). [swissprot;acc:p30154] PPP2R1B Measured 4599.26 1.50373 3058.57
    voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359] CACNG3 Ranked Subtracted 254.693 52.025 202.668
    77 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] no value Measured 20446.1 3690.3 24136.4
    kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] KHDRBS2 Rooted 27.7254 16.3045 44.0299
    myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] no value Squared Divided 110342 1.67024 184298
    sad1/unc-84 protein-like 1. [swissprot;acc:o94901] UNC84A Rooted 39.9725 1.32584 52.9973
    serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, epsilon isoform (pp2a, b subunit, b' epsilon isoform) (pp2a, b subunit, b56 epsilon isoform) (pp2a, b subunit, pr61 epsilon isoform) (pp2a, b subunit, r5 epsilon isoform). [swissprot;acc:q16537] PPP2R5E Squared Subtracted 117718 47212.1 70505.9
    serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [swissprot;acc:p30153] PPP2R1A Measured Divided 4612.39 1.49095 3093.6
    voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698] CACNG2 Ranked 254.692 1.2567 202.668
    Subtracted 52.024
    78 a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] ARAF Squared Divided 117858 1.67008 70570.1
    cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] ATF3 Measured 4800.81 1.48573 7132.71
    cyclin g2. [swissprot;acc:q16589] CCNG2 Squared Subtracted 117718 47212.1 70505.9
    homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] HOXD4 Measured 20446.1 3690.3 24136.4
    nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] no value Rooted 177.987 16.303 194.29
    uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] PPP2R2D Divided 63.7477 1.3237 48.1589
    voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1] CACNG4 Ranked Subtracted 254.691 52.023 202.668
    voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5] CACNG8 Divided 254.693 1.2567
    79 homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] HOXB5 Measured Subtracted 20446.1 3690.3 24136.4
    neuralized-like. [refseq;acc:nm_004210] NEURL Rooted 27.9107 16.2549 44.1656
    protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] UFC1 Measured Divided 3074.57 1.48558 4567.51
    raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] RAF1 Squared 117850 1.67005 70566.8
    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] no value Rooted 63.7477 1.3237 48.1588

    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/