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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 451 to 500 of 29840 in total
    Interaction Map  : High confidence
    Rank
    		description
    		Value Type
    		Network Comparison Type
    		Filtered
    		red
    		green
    		network_comparison
    29 cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946] Rooted Subtracted 0 11.3774 1.80368 9.57372
    galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470] Squared 72128.6 64272.5 7856.1
    guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] Measured Divided 1 1834.52 895.507 2.04858
    guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086] Ranked Subtracted 267.139 336.075 68.936
    melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Measured 23693.7 18263 5430.7
    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] Squared 219048 129762 89286
    microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268] Rooted Divided 0 17.7955 7.34614 2.42243
    phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086] Ranked 7395 11625 1.57201
    potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Measured 111.278 434.911 3.90833
    potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110] Squared 5.18438 141.427 27.2794
    protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] Rooted 1 26.0288 43.1914 1.65937
    putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] Subtracted 210.928 192.165 18.763
    regulator of chromosome condensation (cell cycle regulatory protein). [swissprot;acc:p18754] Measured 0 3248.95 2399.76 849.19
    uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] Ranked Divided 1 187.458 243.678 1.29991
    30 beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938] 0 7395 11625 1.57201
    cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] Measured Subtracted 3265.25 4102.97 837.72
    cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] Rooted 1 60.8022 79.5099 18.7077
    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] Squared Divided 143.692 457.521 3.18404
    dystrophin. [swissprot;acc:p11532] Measured 0 427.217 111.739 3.82335
    guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] 1 1834.59 895.633 2.04837
    guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] Ranked Subtracted 267.14 336.075 68.935
    homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Rooted 0 0 9.43398 9.43398
    lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] Ranked 13730.5 8257 5473.5
    melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Measured 1 23693.7 18263 5430.7
    microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] Rooted Divided 26.0288 43.1914 1.65937
    potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Squared 0 6.25494 141.944 22.6931
    ptd016 protein. [refseq;acc:nm_016125] Rooted 5.47723 12.5698 2.29492
    segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] Squared Subtracted 23310.5 31089.6 7779.1
    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] Ranked Divided 1 187.457 243.678 1.29991
    trophinin. [swissprot;acc:q12816] Squared Subtracted 219048 129762 89286
    31 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] 106226 192141 85915
    beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] Divided 9924.76 25146.6 2.53372
    dok-like protein. [refseq;acc:nm_024872] Measured 0 35 0.00001 3500000
    fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402] Squared 5.54059 103.726 18.7211
    fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] Subtracted 35446.2 27772 7674.2
    guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] Measured Divided 1 1834.63 895.697 2.04827
    guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488] Ranked Subtracted 267.14 336.075 68.935
    homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Rooted 0 0 9.43398 9.43398
    leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735] Ranked Divided 8082.33 5266.67 1.53462
    melanoma antigen, family b, 6. [refseq;acc:nm_173523] Measured Subtracted 1 23693.7 18263 5430.7
    potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110] Ranked 0 11627 6248 5379
    Rooted Divided 12.1655 27.8029 2.28539
    protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] Subtracted 1 40.0958 58.7986 18.7028
    protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] Divided 26.0288 43.1914 1.65937
    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] Ranked 187.458 243.677 1.2999
    spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [swissprot;acc:q13813] Measured Subtracted 0 1833 2637 804
    32 beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] Squared Divided 1 9924.76 25146.6 2.53372
    cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336] Measured 0 598 184 3.25
    ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485] Rooted 1 26.0288 43.1914 1.65937
    gbp protein isoform a. [refseq;acc:nm_017870] Subtracted 23.9771 42.4773 18.5002

    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
    - 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/