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 Network Comparison Type description Hugo Value Type Interaction Map red Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 1001 to 1050 of 66312 in total
    Filtered  : 1
    Rank
    		Network Comparison Type
    		description
    		Hugo
    		Value Type
    		Interaction Map
    		red
    		green
    		network_comparison
    63 Subtracted gdp-mannose pyrophosphorylase a; mannose-1-phosphate guanylyltransferase (gdp). [refseq;acc:nm_013335] GMPPA Squared Low confidence 75927.4 61755.3 14172.1
    jun dimerization protein. [refseq;acc:nm_130469] no value Ranked 202.802 182.73 20.072
    melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] MAGEA10 Rooted High confidence 137.446 120.823 16.623
    nuclear factor erythroid 2 related factor 2 (nf-e2 related factor 2) (nfe2-related factor 2) (nuclear factor, erythroid derived 2, like 2) (hebp1). [swissprot;acc:q16236] NFE2L2 Low confidence 79.2778 86.7076 7.4298
    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] NFYC Ranked High confidence 260.532 204.309 56.223
    ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] RRAGB Measured Low confidence 10618.8 11681.3 1062.5
    serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129] PPP1CA Squared High confidence 189976 124480 65496
    spermatogenesis associated 6. [refseq;acc:nm_019073] SPATA6 Measured 6475.5 10307.5 3832
    64 Divided 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 1.35128
    glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] 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
    neurochondrin. [refseq;acc:nm_014284] NCDN Low confidence 73677.6 57498.7 1.28138
    rab11-family interacting protein 4. [refseq;acc:nm_032932] RAB11FIP4 Rooted 73.6221 81.4944 1.10693
    retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] HSD17B14 Measured 15464.1 17572.7 1.13635
    transcription factor jun-d. [swissprot;acc:p17535] JUND Ranked 202.709 183.361 1.10552
    Subtracted amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] AMPD2 Measured High confidence 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
    fos-related antigen 2. [swissprot;acc:p15408] FOSL2 Ranked Low confidence 202.793 182.961 19.832
    melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] MAGEB4 Rooted High confidence 137.446 120.823 16.623
    ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] RRAGA Measured Low confidence 10585.5 11638.6 1053.1
    septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] SEPT7 Squared 66860.1 80573.4 13713.3
    transcription regulator protein bach2 (btb and cnc homolog 2). [swissprot;acc:q9byv9] BACH2 Rooted 79.2778 86.7076 7.4298
    65 Divided eferin. [swissprot;acc:o75154] RAB11FIP3 73.6221 81.4944 1.10693
    glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] PYGB High confidence 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
    neuralized-like. [refseq;acc:nm_004210] NEURL Measured 1657.68 2690.25 1.6229
    septin 6. [swissprot;acc:q14141] SEPT6 Low confidence 13005.8 14773.7 1.13593
    septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] SEPT8 Squared 75490.8 95493.3 1.26497
    transcription factor jun-b. [swissprot;acc:p17275] JUNB Ranked 202.728 183.388 1.10546
    Subtracted brca1 associated protein. [refseq;acc:nm_006768] BRAP Squared 83524.5 69821.2 13703.3
    cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] CSTF3 Measured High confidence 22515.5 18702.6 3812.9
    dj310o13.4 (novel protein similar to predicted c. elegans and c. intestinalis proteins) (fragment). [sptrembl;acc:q9nug5] XKR7 Rooted Low confidence 75.1927 82.5511 7.3584
    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] MAGED2 High confidence 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
    protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] FOSB Ranked Low confidence 202.792 182.974 19.818
    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] no value High confidence 187.457 243.678 56.221
    thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652] JMJD1C Measured Low confidence 1917.64 2950.5 1032.86
    66 Divided dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] DAB2IP Rooted 55.8923 61.8016 1.10573
    glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] PYGL High confidence 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
    mitochondrial tumor suppressor gene 1; transcription factor mtsg1; at2 receptor-interacting protein 1; erythroid differentiation-related gene. [refseq;acc:nm_020749] MTUS1 Ranked Low confidence 221.902 200.783 1.10518
    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] NDUFA12 Measured High confidence 1991.03 3221.38 1.61795
    septin 10 isoform 1. [refseq;acc:nm_144710] SEPT10 Squared Low confidence 74803.9 94281 1.26038
    son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583] SON Measured 4900.7 5555.81 1.13368
    Subtracted a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] ARAF High confidence 17757.5 14008 3749.5
    fos-related antigen 1 (fra-1). [swissprot;acc:p15407] FOSL1 Ranked Low confidence 202.79 183.017 19.773

    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/