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 Value Type Network Comparison Type Interaction Map red Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 501 to 550 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		Network Comparison Type
    		red
    		green
    		network_comparison
    63 MYO15A myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] Measured Divided 4489.19 2765.82 1.6231
    NFYC nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952] Ranked Subtracted 260.532 204.309 56.223
    PPP1CA serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129] Squared 189976 124480 65496
    SPATA6 spermatogenesis associated 6. [refseq;acc:nm_019073] Measured 6475.5 10307.5 3832
    64 AMPD2 amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]
    ATG4A cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] Squared 144940 81169.7 63770.3
    GBE1 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] Rooted Divided 63.8686 47.2654 1.35128
    GNG11 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] Ranked 266.868 336.159 1.25965
    MAGEB4 melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] Rooted Subtracted 137.446 120.823 16.623
    MAGEB6B melanoma antigen, family b, 6. [refseq;acc:nm_173523] Squared Divided 219048 129762 1.68808
    NFYA ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511] Ranked Subtracted 260.532 204.309 56.223
    PYGM glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] Measured Divided 4489.19 2765.82 1.6231
    65 no value melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] Squared 219048 129762 1.68808
    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 Subtracted 187.457 243.678 56.221
    CSTF3 cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] Measured 22515.5 18702.6 3812.9
    GNAQ guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] Ranked Divided 267.136 336.077 1.25807
    MAGED2 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] Rooted Subtracted 137.446 120.823 16.623
    MAP1LC3B microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] Squared 144912 81155 63757
    NEURL neuralized-like. [refseq;acc:nm_004210] Measured Divided 1657.68 2690.25 1.6229
    PYGB glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] Rooted 63.8686 47.2654 1.35128
    66 ARAF a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] Measured Subtracted 17757.5 14008 3749.5
    GNA11 guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] Ranked Divided 267.136 336.077 1.25807
    MAGEA9 melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] Squared 219048 129762 1.68808
    MAP1LC3A microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Subtracted 144911 81154.7 63756.3
    NDUFA12 nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09] Measured Divided 1991.03 3221.38 1.61795
    PPP2R2D uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] Ranked Subtracted 187.458 243.678 56.22
    PYGL glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] Rooted Divided 63.8686 47.2654 1.35128
    TRO trophinin. [swissprot;acc:q12816] Subtracted 137.446 120.823 16.623
    67 ARRB2 beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] Measured Divided 6475.5 10307.5 1.59177
    ATG4B cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Squared Subtracted 144876 81136.5 63739.5
    GBE1 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] Rooted 63.8686 47.2654 16.6032
    GNAT2 guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] Ranked Divided 267.14 336.075 1.25805
    MAGEA8 melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] Squared 219048 129762 1.68808
    MYO15A myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] Rooted 63.8686 47.2654 1.35128
    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] Ranked Subtracted 187.458 243.677 56.219
    RAF1 raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] Measured 17756.5 14007.3 3749.2
    68 ARRB1 beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] Divided 6475.5 10307.5 1.59177
    CCNG2 cyclin g2. [swissprot;acc:q16589] Subtracted 17738.6 13995.7 3742.9
    GABARAP gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] Squared 139741 78454.6 61286.4
    GNAZ guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086] Ranked Divided 267.139 336.075 1.25805
    MAGEC1 melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] Squared 219048 129762 1.68808
    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] Ranked Subtracted 187.462 243.673 56.211
    PYGB glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] Rooted 63.8686 47.2654 16.6032
    PYGM glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] Divided 1.35128
    69 CCNG1 cyclin g1 (cyclin g). [swissprot;acc:p51959] Measured Subtracted 17738.5 13995.6 3742.9
    GNAT1 guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488] Ranked Divided 267.14 336.075 1.25805
    MAGEA4 melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] Squared 219048 129762 1.68808
    NDUFA12 nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09] Ranked Subtracted 284.753 228.934 55.819
    NEUROD2 neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] Rooted Divided 27.9136 37.2872 1.33581
    PCF11 pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913] Squared Subtracted 178263 118639 59624

    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/