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 Network Comparison Type Hugo Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 501 to 550 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Network Comparison Type
    		Hugo
    		Value Type
    		red
    		green
    		network_comparison
    63 myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] Divided MYO15A Measured 4489.19 2765.82 1.6231
    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] Subtracted NFYC Ranked 260.532 204.309 56.223
    serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129] PPP1CA Squared 189976 124480 65496
    spermatogenesis associated 6. [refseq;acc:nm_019073] SPATA6 Measured 6475.5 10307.5 3832
    64 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] Divided GBE1 Rooted 63.8686 47.2654 1.35128
    amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] Subtracted AMPD2 Measured 6475.5 10307.5 3832
    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] NFYA Ranked 260.532 204.309 56.223
    cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] ATG4A Squared 144940 81169.7 63770.3
    glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] Divided PYGM Measured 4489.19 2765.82 1.6231
    guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] GNG11 Ranked 266.868 336.159 1.25965
    melanoma antigen, family b, 6. [refseq;acc:nm_173523] MAGEB6B Squared 219048 129762 1.68808
    melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] Subtracted MAGEB4 Rooted 137.446 120.823 16.623
    65 cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] CSTF3 Measured 22515.5 18702.6 3812.9
    glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] Divided PYGB Rooted 63.8686 47.2654 1.35128
    guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] GNAQ Ranked 267.136 336.077 1.25807
    melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] no value Squared 219048 129762 1.68808
    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] Subtracted MAGED2 Rooted 137.446 120.823 16.623
    microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] MAP1LC3B Squared 144912 81155 63757
    neuralized-like. [refseq;acc:nm_004210] Divided NEURL Measured 1657.68 2690.25 1.6229
    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] Subtracted no value Ranked 187.457 243.678 56.221
    66 a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] ARAF Measured 17757.5 14008 3749.5
    glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] Divided PYGL Rooted 63.8686 47.2654 1.35128
    guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] GNA11 Ranked 267.136 336.077 1.25807
    melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] MAGEA9 Squared 219048 129762 1.68808
    microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Subtracted MAP1LC3A 144911 81154.7 63756.3
    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] Divided NDUFA12 Measured 1991.03 3221.38 1.61795
    trophinin. [swissprot;acc:q12816] Subtracted TRO Rooted 137.446 120.823 16.623
    uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] PPP2R2D Ranked 187.458 243.678 56.22
    67 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] GBE1 Rooted 63.8686 47.2654 16.6032
    beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] Divided ARRB2 Measured 6475.5 10307.5 1.59177
    cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Subtracted ATG4B Squared 144876 81136.5 63739.5
    guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] Divided GNAT2 Ranked 267.14 336.075 1.25805
    melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] MAGEA8 Squared 219048 129762 1.68808
    myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] MYO15A Rooted 63.8686 47.2654 1.35128
    raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] Subtracted RAF1 Measured 17756.5 14007.3 3749.2
    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 Ranked 187.458 243.677 56.219
    68 beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] Divided ARRB1 Measured 6475.5 10307.5 1.59177
    cyclin g2. [swissprot;acc:q16589] Subtracted CCNG2 17738.6 13995.7 3742.9
    gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] GABARAP Squared 139741 78454.6 61286.4
    glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] PYGB Rooted 63.8686 47.2654 16.6032
    glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] Divided PYGM 1.35128
    guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086] GNAZ Ranked 267.139 336.075 1.25805
    melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] MAGEC1 Squared 219048 129762 1.68808
    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] Subtracted PPP2R2C Ranked 187.462 243.673 56.211
    69 cyclin g1 (cyclin g). [swissprot;acc:p51959] CCNG1 Measured 17738.5 13995.6 3742.9
    glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] PYGL Rooted 63.8686 47.2654 16.6032
    guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488] Divided GNAT1 Ranked 267.14 336.075 1.25805
    melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] MAGEA4 Squared 219048 129762 1.68808
    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] Subtracted NDUFA12 Ranked 284.753 228.934 55.819
    neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] Divided NEUROD2 Rooted 27.9136 37.2872 1.33581

    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/