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 [...,...].
    Gene Rank Filtered Value Type description Network Comparison Type green Interaction Map red network_comparison
    Results: HTML CSV LaTeX Showing element 501 to 550 of 38536 in total
    Network Comparison Type  : Divided
    Rank
    		Filtered
    		Value Type
    		description
    		green
    		Interaction Map
    		red
    		network_comparison
    32 0 Squared melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] 0.355148 Low confidence 3.41692 9.62112
    phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086] 4.57302 High confidence 76.8994 16.8159
    Rooted melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] 5.80678 Low confidence 9.84765 1.69589
    ubiquitin protein ligase. [refseq;acc:nm_130466] 11.258 High confidence 24.0391 2.13529
    1 Measured guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] 895.893 1834.73 2.04793
    nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] 43368.8 Low confidence 36360.3 1.19275
    Ranked protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] 232.49 273.188 1.17505
    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] 243.673 High confidence 187.462 1.29985
    Squared beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] 25146.6 9924.76 2.53372
    melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] 61881.5 Low confidence 82347.8 1.33073
    Rooted ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485] 43.1914 High confidence 26.0288 1.65937
    mitochondrial solute carrier protein. [refseq;acc:nm_145305] 168.796 Low confidence 145.551 1.1597
    33 0 Measured lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893] 39.8063 High confidence 12.6208 3.15402
    melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] 35.5 Low confidence 105.5 2.97183
    Ranked fk506-binding protein 6 (ec 5.2.1.8) (peptidyl-prolyl cis-trans isomerase) (ppiase) (rotamase) (36 kda fk506 binding protein) (fkbp- 36) (immunophilin fkbp36). [swissprot;acc:o75344] 14746.1 20324.1 1.37827
    nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [swissprot;acc:q99733] 8691.76 High confidence 13292.2 1.52929
    Squared beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938] 4.57302 76.8994 16.8159
    melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] 0.355148 Low confidence 3.41692 9.62112
    Rooted fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402] 25.7294 High confidence 12.3693 2.0801
    melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] 5.80678 Low confidence 9.84765 1.69589
    1 Measured guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] 896.972 High confidence 1835.3 2.04611
    vitelliform macular dystrophy 2-like protein 1. [refseq;acc:nm_017682] 43368.8 Low confidence 36360.3 1.19275
    Ranked dual specificity mitogen-activated protein kinase kinase 4 (ec 2.7.1.-) (map kinase kinase 4) (jnk activating kinase 1) (c-jun n- terminal kinase kinase 1) (jnkk) (sapk/erk kinase 1) (sek1). [swissprot;acc:p45985] 246.125 210.241 1.17068
    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] 242.742 High confidence 188.688 1.28647
    Squared hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] 61881.5 Low confidence 82347.8 1.33073
    spermatogenesis associated 6. [refseq;acc:nm_019073] 25146.6 High confidence 9924.76 2.53372
    Rooted protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] 43.1914 26.0288 1.65937
    retinoblastoma-associated factor 600. [refseq;acc:nm_020765] 88.6244 Low confidence 76.5734 1.15738
    34 0 Measured glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926] 47 High confidence 143 3.04255
    melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] 35.5 Low confidence 105.5 2.97183
    Ranked fibrillin 3. [refseq;acc:nm_032447] 7506.66 5450.5 1.37724
    microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268] 17173.8 High confidence 11284 1.52196
    Squared lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893] 0.697197 0.0435834 15.9968
    melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] 0.355148 Low confidence 3.41692 9.62112
    Rooted melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] 5.80678 9.84765 1.69589
    phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086] 11.7898 High confidence 23.8747 2.02503
    1 Measured guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] 907.546 1836.71 2.02382
    protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] 6352.4 Low confidence 5339.5 1.1897
    Ranked putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] 133.876 155.56 1.16197
    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] 242.453 High confidence 189.07 1.28235
    Squared amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] 25146.6 9924.76 2.53372
    melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] 61881.5 Low confidence 82347.8 1.33073
    Rooted guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] 24.3678 High confidence 40.2812 1.65305
    putative rna-binding protein 7 (rna binding motif protein 7). [swissprot;acc:q9y580] 56.755 Low confidence 49.0544 1.15698
    35 0 Measured adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236] 1377 High confidence 459.5 2.99674
    melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] 35.5 Low confidence 105.5 2.97183
    Ranked nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] 4871.6 High confidence 3208.8 1.5182
    protein tyrosine phosphatase type iva, member 2 isoform 1; protein tyrosine phosphatase iva2; protein tyrosine phosphatase iva; phosphatase of regenerating liver 2. [refseq;acc:nm_003479] 16243 Low confidence 11808.5 1.37553
    Squared adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236] 647.816 High confidence 50.7031 12.7767
    melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] 0.355148 Low confidence 3.41692 9.62112

    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/