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 Hugo Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 94 to 143 of 6456 in total
    Value Type  : Ranked
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Network Comparison Type
    		red
    		green
    		network_comparison
    47 tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] TOB2 Subtracted 350 290 60
    48 gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] GABARAP Divided 65.4586 83.0461 1.26868
    tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] TOB1 Subtracted 350 290 60
    49 beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] ARRB2 Divided 133 105 1.26667
    dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] DAB2IP Subtracted 350 290 60
    50 beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] ARRB1 Divided 133 105 1.26667
    cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] CPEB4 Subtracted 350 290 60
    51 cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] CPEB3
    spermatogenesis associated 6. [refseq;acc:nm_019073] SPATA6 Divided 133 105 1.26667
    52 amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] AMPD2
    ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] RASAL2 Subtracted 350 290 60
    53 nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181] NDUFS4 318.982 259.004 59.978
    transcription factor jun-b. [swissprot;acc:p17275] JUNB Divided 201.144 158.868 1.26611
    54 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] GBE1 Subtracted 185.678 245.247 59.569
    transcription factor jun-d. [swissprot;acc:p17535] JUND Divided 200.941 158.941 1.26425
    55 glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] PYGB Subtracted 185.678 245.247 59.569
    protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] PRKRAP1 Divided 320.927 254.434 1.26134
    56 glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] PYGL Subtracted 185.678 245.247 59.569
    guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] no value Divided 266.856 336.233 1.25998
    57 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] GNG12
    myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] MYO15A Subtracted 185.678 245.247 59.569
    58 glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] PYGM
    guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] GNG4 Divided 266.863 336.191 1.25979
    59 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] GNG3 336.19 1.25978
    potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] KCND2 Subtracted 269.278 327.709 58.431
    60 cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] CTH 269.254 327.655 58.401
    guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] GNG8 Divided 266.864 336.184 1.25976
    61 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] GNG5 336.182 1.25975
    potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980] KCND3 Subtracted 269.248 327.642 58.394
    62 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] GNG10 Divided 266.865 336.181 1.25974
    potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] KCND1 Subtracted 269.23 327.601 58.371
    63 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] no value Divided 266.865 336.178 1.25973
    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 Subtracted 260.532 204.309 56.223
    64 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
    guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] GNG11 Divided 266.868 336.159 1.25965
    65 guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] GNAQ 267.136 336.077 1.25807
    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 Subtracted 187.457 243.678 56.221
    66 guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] GNA11 Divided 267.136 336.077 1.25807
    uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] PPP2R2D Subtracted 187.458 243.678 56.22
    67 guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] GNAT2 Divided 267.14 336.075 1.25805
    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 Subtracted 187.458 243.677 56.219
    68 guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086] GNAZ Divided 267.139 336.075 1.25805
    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] PPP2R2C Subtracted 187.462 243.673 56.211
    69 guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488] GNAT1 Divided 267.14 336.075 1.25805
    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 Subtracted 284.753 228.934 55.819
    70 guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899] GNAI2 Divided 267.142 336.074 1.25804
    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] PPP2R1B Subtracted 188.688 242.742 54.054
    71 guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898] GNAI1 Divided 267.144 336.073 1.25802
    kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] KCNIP1 Subtracted 265.686 319.651 53.965
    72 guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754] GNAI3 Divided 267.144 336.073 1.25802

    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/