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 Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 143 to 192 of 6456 in total
    Value Type  : Measured
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Network Comparison Type
    		red
    		green
    		network_comparison
    72 b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056] Subtracted 17710.9 13977.7 3733.2
    uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] Divided 4556.79 2945.28 1.54715
    73 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] 4556.83 2945.38 1.54711
    serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] Subtracted 22268.8 18560.4 3708.4
    74 homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 20446.1 24136.4 3690.3
    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] Divided 4556.99 2945.8 1.54694
    75 homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] Subtracted 20446.1 24136.4 3690.3
    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] Divided 1920.75 2907.43 1.5137
    76 homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Subtracted 20446.1 24136.4 3690.3
    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] Divided 4599.26 3058.57 1.50373
    77 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Subtracted 20446.1 24136.4 3690.3
    serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [swissprot;acc:p30153] Divided 4612.39 3093.6 1.49095
    78 cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] 4800.81 7132.71 1.48573
    homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Subtracted 20446.1 24136.4 3690.3
    79 homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067]
    protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] Divided 3074.57 4567.51 1.48558
    80 homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] Subtracted 20446.1 24136.4 3690.3
    nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] Divided 4133.47 5945.32 1.43834
    81 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Subtracted 20446.1 24136.4 3690.3
    nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] Divided 4136.36 5943.56 1.43691
    82 retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] Subtracted 20446.1 24136.4 3690.3
    small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Divided 4172.91 5954.48 1.42694
    83 protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] Subtracted 21644.2 18098.7 3545.5
    proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] Divided 4932.27 7033.29 1.42597
    84 jun dimerization protein. [refseq;acc:nm_130469]
    type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] Subtracted 21632.5 18090 3542.5
    85 fos-related antigen 2. [swissprot;acc:p15408] Divided 4941.95 7037.11 1.42395
    ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050] Subtracted 21370.8 17896.5 3474.3
    86 protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] Divided 4942.49 7037.32 1.42384
    serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129] Subtracted 21370.8 17896.5 3474.3
    87 fos-related antigen 1 (fra-1). [swissprot;acc:p15407] Divided 4944.3 7038.04 1.42347
    pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913] Subtracted 20287.2 17083.8 3203.4
    88 potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Divided 2411.93 1695.45 1.42259
    transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116] Subtracted 16074 12888.4 3185.6
    89 cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] Divided 2414.22 1698.12 1.4217
    leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13] Subtracted 16071.6 12886.8 3184.8
    90 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] Divided 2414.77 1698.75 1.4215
    ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211] Subtracted 16071.6 12886.8 3184.8
    91 potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] Divided 2416.53 1700.8 1.42082
    transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112] Subtracted 16070.4 12886 3184.4
    92 dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Divided 4117.67 5801.04 1.40882
    transforming protein n-ras. [swissprot;acc:p01111] Subtracted 16069.8 12885.6 3184.2
    93 formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] Divided 4245.52 5942.75 1.39977
    sedlin. [swissprot;acc:o14582] Subtracted 17396.9 20483.9 3087
    94 huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] Divided 4247.86 5941.88 1.39879
    synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] Subtracted 17396.9 20483.9 3087
    95 bet3 homolog. [swissprot;acc:o43617]
    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] Divided 2397.19 3343.62 1.39481
    96 lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] 4110.14 5694.99 1.3856
    septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] Subtracted 16177.9 19235.4 3057.5

    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/