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 Filtered network_comparison Interaction Map red green
    Results: HTML CSV LaTeX Showing element 501 to 550 of 38536 in total
    Network Comparison Type  : Divided
    Rank
    		description
    		Value Type
    		Filtered
    		network_comparison
    		Interaction Map
    		red
    		green
    32 importin 9. [refseq;acc:nm_018085] Ranked 0 1.52929 High confidence 13292.2 8691.76
    melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] Rooted 1.69589 Low confidence 9.84765 5.80678
    melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] Squared 1 1.33073 82347.8 61881.5
    melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Measured 0 2.97183 105.5 35.5
    melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Squared 9.62112 3.41692 0.355148
    mitochondrial solute carrier protein. [refseq;acc:nm_145305] Rooted 1 1.1597 145.551 168.796
    myoglobin. [swissprot;acc:p02144] Ranked 0 1.39162 11485.4 15983.3
    nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Measured 1 1.19275 36360.3 43368.8
    phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086] Squared 0 16.8159 High confidence 76.8994 4.57302
    protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] Ranked 1 1.17505 Low confidence 273.188 232.49
    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] 1.29985 High confidence 187.462 243.673
    ubiquitin protein ligase. [refseq;acc:nm_130466] Rooted 0 2.13529 24.0391 11.258
    33 beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938] Squared 16.8159 76.8994 4.57302
    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] Ranked 1 1.17068 Low confidence 210.241 246.125
    fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402] Rooted 0 2.0801 High confidence 12.3693 25.7294
    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] Ranked 1.37827 Low confidence 20324.1 14746.1
    guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] Measured 1 2.04611 High confidence 1835.3 896.972
    hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] Squared 1.33073 Low confidence 82347.8 61881.5
    lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893] Measured 0 3.15402 High confidence 12.6208 39.8063
    melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] Rooted 1.69589 Low confidence 9.84765 5.80678
    melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] Squared 9.62112 3.41692 0.355148
    melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Measured 2.97183 105.5 35.5
    nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [swissprot;acc:q99733] Ranked 1.52929 High confidence 13292.2 8691.76
    protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] Rooted 1 1.65937 26.0288 43.1914
    retinoblastoma-associated factor 600. [refseq;acc:nm_020765] 1.15738 Low confidence 76.5734 88.6244
    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] Ranked 1.28647 High confidence 188.688 242.742
    spermatogenesis associated 6. [refseq;acc:nm_019073] Squared 2.53372 9924.76 25146.6
    vitelliform macular dystrophy 2-like protein 1. [refseq;acc:nm_017682] Measured 1.19275 Low confidence 36360.3 43368.8
    34 amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] Squared 2.53372 High confidence 9924.76 25146.6
    fibrillin 3. [refseq;acc:nm_032447] Ranked 0 1.37724 Low confidence 5450.5 7506.66
    glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926] Measured 3.04255 High confidence 143 47
    guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] 1 2.02382 1836.71 907.546
    Rooted 1.65305 40.2812 24.3678
    lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893] Squared 0 15.9968 0.0435834 0.697197
    melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] Rooted 1.69589 Low confidence 9.84765 5.80678
    melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Squared 1 1.33073 82347.8 61881.5
    melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] 0 9.62112 3.41692 0.355148
    melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Measured 2.97183 105.5 35.5
    microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268] Ranked 1.52196 High confidence 11284 17173.8
    phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086] Rooted 2.02503 23.8747 11.7898
    protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] Measured 1 1.1897 Low confidence 5339.5 6352.4
    putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] Ranked 1.16197 155.56 133.876
    putative rna-binding protein 7 (rna binding motif protein 7). [swissprot;acc:q9y580] Rooted 1.15698 49.0544 56.755
    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] Ranked 1.28235 High confidence 189.07 242.453
    35 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] Squared 1.80879 106226 192141
    adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236] Measured 0 2.99674 459.5 1377
    Squared 12.7767 50.7031 647.816
    beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938] Rooted 2.02503 23.8747 11.7898
    deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] Measured 1 1.18866 Low confidence 33111.4 39358.1
    guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] 2.02378 High confidence 1836.71 907.564

    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/