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 Network Comparison Type Value Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 2362 to 2411 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Value Type
    		red
    		network_comparison
    		green
    591 homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356] HOXD9 Measured 6740.5 1.13415 7644.76
    leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13] SHOC2 Rooted 108.659 1.08274 100.356
    ribonuclease p protein subunit p30 (ec 3.1.26.5) (rnasep protein p30) (rnase p subunit 2). [swissprot;acc:p78346] RPP30 Ranked 216.72 1.0633 230.439
    592 histone h2b.c (h2b/c). [swissprot;acc:q99880] HIST1H2BL Measured 3946.32 1.13409 4475.47
    protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712] PPP1R7 Ranked 91.63 1.06298 97.4011
    ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211] no value Rooted 108.659 1.08274 100.356
    voltage-gated potassium channel beta-2 subunit (k+ channel beta-2 subunit) (kv-beta-2) (hkvbeta2). [swissprot;acc:q13303] KCNAB2 Squared 23526.4 1.18502 27879.3
    593 aflatoxin b1 aldehyde reductase 1 (ec 1.-.-.-) (afb1-ar 1) (aldoketoreductase 7). [swissprot;acc:o43488] AKR7A2
    histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778] HIST2H2BA Measured 3946.32 1.13409 4475.47
    tata-binding protein-associated phosphoprotein (down-regulator of transcription 1) (dr1 protein). [swissprot;acc:q01658] DR1 Ranked 232.118 1.06278 218.406
    transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112] HRAS Rooted 108.653 1.08272 100.352
    594 histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106] no value Measured 3946.32 1.13409 4475.47
    importin alpha-1 subunit (karyopherin alpha-1 subunit) (srp1-beta) (rag cohort protein 2) (nucleoprotein interactor 1) (npi-1). [swissprot;acc:p52294] KPNA1 Squared 23517.1 1.18498 27867.3
    pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508] CDC40 Ranked 223.282 1.06256 210.136
    transforming protein n-ras. [swissprot;acc:p01111] no value Rooted 108.65 1.08271 100.35
    595 5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646] PRKAA2 Squared 34129.7 1.18474 40434.8
    fibrillarin (34 kda nucleolar scleroderma antigen). [swissprot;acc:p22087] FBL Rooted 51.2427 1.08246 55.468
    histone h2b. [refseq;acc:nm_175055] no value Measured 3946.32 1.13409 4475.47
    vav proto-oncogene. [swissprot;acc:p15498] VAV1 Ranked 212.2 1.0618 199.849
    596 5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619] PRKAG1 Squared 34129.6 1.18473 40434.5
    cbf1 interacting corepressor. [refseq;acc:nm_004882] no value Rooted 60.0587 1.08237 65.0057
    histone h2b.s (h2b/s). [swissprot;acc:p57053] Measured 3946.32 1.13409 4475.47
    vav-3 protein. [swissprot;acc:q9ukw4] VAV3 Ranked 212.253 1.06175 199.908
    597 5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131] PRKAA1 Squared 34129.4 1.18473 40434.2
    evolutionarily conserved g-patch domain containing. [refseq;acc:nm_018025] GPATCH1 Rooted 60.0587 1.08237 65.0057
    histone h2b.d (h2b/d). [swissprot;acc:q99877] no value Measured 3946.32 1.13409 4475.47
    vav-2 protein. [swissprot;acc:p52735] VAV2 Ranked 212.526 1.0615 200.212
    598 5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741] PRKAB2 Squared 34129.6 1.18473 40434.5
    histone h3.4 (h3t) (h3/t) (h3/g). [swissprot;acc:q16695] HIST3H3 Measured 3946.32 1.13409 4475.47
    methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192] MARS Rooted 61.2527 1.08182 66.2644
    rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [swissprot;acc:p31749] AKT1 Ranked 248.463 1.06138 234.095
    599 5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9] PRKAG3 Squared 34129.6 1.18473 40434.5
    cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693] CPSF4 Rooted 138.375 1.08168 127.926
    rac-gamma serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-gamma) (protein kinase akt-3) (protein kinase b, gamma) (pkb gamma) (stk-2). [swissprot;acc:q9y243] AKT3 Ranked 248.463 1.06138 234.095
    testis-specific histone h2b; h2b histone family, member u, (testis-specific). [refseq;acc:nm_170610] HIST1H2BA Measured 3946.32 1.13409 4475.47
    600 5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478] PRKAB1 Squared 34129.6 1.18473 40434.5
    histone h2b.e (h2b/e). [swissprot;acc:q99879] no value Measured 3946.32 1.13409 4475.47
    rac-beta serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-beta) (protein kinase akt-2) (protein kinase b, beta) (pkb beta). [swissprot;acc:p31751] AKT2 Ranked 248.463 1.06138 234.095
    trs85 homolog. [swissprot;acc:q9y2l5] KIAA1012 Rooted 138.375 1.08168 127.926
    601 5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0] PRKAG2 Squared 34129.6 1.18473 40434.5
    symplekin. [swissprot;acc:q92797] SYMPK Measured 15213.4 1.1338 13418.1
    vam6/vps39-like protein (hvam6p). [swissprot;acc:q96jc1] VPS39 Ranked 206.274 1.06069 218.792
    wd-repeat protein wdc146. [swissprot;acc:q9c0j8] WDR33 Rooted 138.032 1.08132 127.651
    602 ataxin 2 related protein isoform a; ataxin-2 domain protein. [refseq;acc:nm_007245] ATXN2L Measured 4864.66 1.13366 5514.87
    cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] CPSF1 Rooted 138.032 1.08132 127.651
    microtubule-associated protein 4 (map 4). [swissprot;acc:p27816] MAP4 Ranked 206.274 1.06069 218.792
    spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] TXNL4A Squared 19129.8 1.18417 22652.9
    603 ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] no value Measured 4864.66 1.13366 5514.87
    lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [swissprot;acc:q9uju2] LEF1 Ranked 225.829 1.0605 212.945
    nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594] no value Squared 34071.5 1.18388 40336.5

    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
    - 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/