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 Value Type red green description Network Comparison Type Interaction Map Filtered network_comparison
    Results: HTML CSV LaTeX Showing element 501 to 550 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Value Type
    		red
    		green
    		description
    		Network Comparison Type
    		network_comparison
    63 Squared 189976 124480 serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129] Subtracted 65496
    219048 129762 melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Divided 1.68808
    Rooted 43.4554 31.7576 kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193] 1.36835
    137.446 120.823 melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Subtracted 16.623
    64 Measured 4489.19 2765.82 glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] Divided 1.6231
    6475.5 10307.5 amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] Subtracted 3832
    Ranked 260.532 204.309 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] 56.223
    266.868 336.159 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] Divided 1.25965
    Squared 144940 81169.7 cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] Subtracted 63770.3
    219048 129762 melanoma antigen, family b, 6. [refseq;acc:nm_173523] Divided 1.68808
    Rooted 63.8686 47.2654 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] 1.35128
    137.446 120.823 melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] Subtracted 16.623
    65 Measured 1657.68 2690.25 neuralized-like. [refseq;acc:nm_004210] Divided 1.6229
    22515.5 18702.6 cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] Subtracted 3812.9
    Ranked 187.457 243.678 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] 56.221
    267.136 336.077 guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] Divided 1.25807
    Squared 144912 81155 microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] Subtracted 63757
    219048 129762 melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] Divided 1.68808
    Rooted 63.8686 47.2654 glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] 1.35128
    137.446 120.823 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 16.623
    66 Measured 1991.03 3221.38 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 1.61795
    17757.5 14008 a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] Subtracted 3749.5
    Ranked 187.458 243.678 uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] 56.22
    267.136 336.077 guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] Divided 1.25807
    Squared 144911 81154.7 microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Subtracted 63756.3
    219048 129762 melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] Divided 1.68808
    Rooted 63.8686 47.2654 glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] 1.35128
    137.446 120.823 trophinin. [swissprot;acc:q12816] Subtracted 16.623
    67 Measured 6475.5 10307.5 beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] Divided 1.59177
    17756.5 14007.3 raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] Subtracted 3749.2
    Ranked 187.458 243.677 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] 56.219
    267.14 336.075 guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] Divided 1.25805
    Squared 144876 81136.5 cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Subtracted 63739.5
    219048 129762 melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] Divided 1.68808
    Rooted 63.8686 47.2654 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] Subtracted 16.6032
    myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] Divided 1.35128
    68 Measured 6475.5 10307.5 beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] 1.59177
    17738.6 13995.7 cyclin g2. [swissprot;acc:q16589] Subtracted 3742.9
    Ranked 187.462 243.673 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] 56.211
    267.139 336.075 guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086] Divided 1.25805
    Squared 139741 78454.6 gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] Subtracted 61286.4
    219048 129762 melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] Divided 1.68808
    Rooted 63.8686 47.2654 glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] Subtracted 16.6032
    glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] Divided 1.35128
    69 Measured 6475.5 10307.5 spermatogenesis associated 6. [refseq;acc:nm_019073] 1.59177
    17738.5 13995.6 cyclin g1 (cyclin g). [swissprot;acc:p51959] Subtracted 3742.9
    Ranked 267.14 336.075 guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488] Divided 1.25805
    284.753 228.934 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 55.819
    Squared 178263 118639 pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913] 59624
    219048 129762 melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] Divided 1.68808

    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/