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 Hugo description Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2358 to 2407 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		red
    		green
    		network_comparison
    590 PDXDC1 similar to expressed sequence aa415817. [sptrembl;acc:q8n4q9] Measured 6739.85 7644.63 1.13424
    REXO2 oligoribonuclease, mitochondrial precursor (ec 3.1.-.-) (small fragment nuclease) (cgi-114). [swissprot;acc:q9y3b8] Squared 23526.4 27879.3 1.18502
    RRM1 ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] Ranked 217.215 204.279 1.06333
    591 CHAT choline o-acetyltransferase (ec 2.3.1.6) (choactase) (choline acetylase) (chat). [swissprot;acc:p28329] Squared 23526.5 27879.4 1.18502
    HOXD9 homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356] Measured 6740.5 7644.76 1.13415
    RPP30 ribonuclease p protein subunit p30 (ec 3.1.26.5) (rnasep protein p30) (rnase p subunit 2). [swissprot;acc:p78346] Ranked 216.72 230.439 1.0633
    SHOC2 leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13] Rooted 108.659 100.356 1.08274
    592 no value ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211]
    HIST1H2BL histone h2b.c (h2b/c). [swissprot;acc:q99880] Measured 3946.32 4475.47 1.13409
    KCNAB2 voltage-gated potassium channel beta-2 subunit (k+ channel beta-2 subunit) (kv-beta-2) (hkvbeta2). [swissprot;acc:q13303] Squared 23526.4 27879.3 1.18502
    PPP1R7 protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712] Ranked 91.63 97.4011 1.06298
    593 AKR7A2 aflatoxin b1 aldehyde reductase 1 (ec 1.-.-.-) (afb1-ar 1) (aldoketoreductase 7). [swissprot;acc:o43488] Squared 23526.4 27879.3 1.18502
    DR1 tata-binding protein-associated phosphoprotein (down-regulator of transcription 1) (dr1 protein). [swissprot;acc:q01658] Ranked 232.118 218.406 1.06278
    HIST2H2BA histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778] Measured 3946.32 4475.47 1.13409
    HRAS transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112] Rooted 108.653 100.352 1.08272
    594 no value histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106] Measured 3946.32 4475.47 1.13409
    transforming protein n-ras. [swissprot;acc:p01111] Rooted 108.65 100.35 1.08271
    CDC40 pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508] Ranked 223.282 210.136 1.06256
    KPNA1 importin alpha-1 subunit (karyopherin alpha-1 subunit) (srp1-beta) (rag cohort protein 2) (nucleoprotein interactor 1) (npi-1). [swissprot;acc:p52294] Squared 23517.1 27867.3 1.18498
    595 no value histone h2b. [refseq;acc:nm_175055] Measured 3946.32 4475.47 1.13409
    FBL fibrillarin (34 kda nucleolar scleroderma antigen). [swissprot;acc:p22087] Rooted 51.2427 55.468 1.08246
    PRKAA2 5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646] Squared 34129.7 40434.8 1.18474
    VAV1 vav proto-oncogene. [swissprot;acc:p15498] Ranked 212.2 199.849 1.0618
    596 no value cbf1 interacting corepressor. [refseq;acc:nm_004882] Rooted 60.0587 65.0057 1.08237
    histone h2b.s (h2b/s). [swissprot;acc:p57053] Measured 3946.32 4475.47 1.13409
    PRKAG1 5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619] Squared 34129.6 40434.5 1.18473
    VAV3 vav-3 protein. [swissprot;acc:q9ukw4] Ranked 212.253 199.908 1.06175
    597 no value histone h2b.d (h2b/d). [swissprot;acc:q99877] Measured 3946.32 4475.47 1.13409
    GPATCH1 evolutionarily conserved g-patch domain containing. [refseq;acc:nm_018025] Rooted 60.0587 65.0057 1.08237
    PRKAA1 5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131] Squared 34129.4 40434.2 1.18473
    VAV2 vav-2 protein. [swissprot;acc:p52735] Ranked 212.526 200.212 1.0615
    598 AKT1 rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [swissprot;acc:p31749] 248.463 234.095 1.06138
    HIST3H3 histone h3.4 (h3t) (h3/t) (h3/g). [swissprot;acc:q16695] Measured 3946.32 4475.47 1.13409
    MARS methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192] Rooted 61.2527 66.2644 1.08182
    PRKAB2 5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741] Squared 34129.6 40434.5 1.18473
    599 AKT3 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] Ranked 248.463 234.095 1.06138
    CPSF4 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] Rooted 138.375 127.926 1.08168
    HIST1H2BA testis-specific histone h2b; h2b histone family, member u, (testis-specific). [refseq;acc:nm_170610] Measured 3946.32 4475.47 1.13409
    PRKAG3 5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9] Squared 34129.6 40434.5 1.18473
    600 no value histone h2b.e (h2b/e). [swissprot;acc:q99879] Measured 3946.32 4475.47 1.13409
    AKT2 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] Ranked 248.463 234.095 1.06138
    KIAA1012 trs85 homolog. [swissprot;acc:q9y2l5] Rooted 138.375 127.926 1.08168
    PRKAB1 5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478] Squared 34129.6 40434.5 1.18473
    601 PRKAG2 5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0]
    SYMPK symplekin. [swissprot;acc:q92797] Measured 15213.4 13418.1 1.1338
    VPS39 vam6/vps39-like protein (hvam6p). [swissprot;acc:q96jc1] Ranked 206.274 218.792 1.06069
    WDR33 wd-repeat protein wdc146. [swissprot;acc:q9c0j8] Rooted 138.032 127.651 1.08132
    602 ATXN2L ataxin 2 related protein isoform a; ataxin-2 domain protein. [refseq;acc:nm_007245] Measured 4864.66 5514.87 1.13366
    CPSF1 cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] Rooted 138.032 127.651 1.08132
    MAP4 microtubule-associated protein 4 (map 4). [swissprot;acc:p27816] Ranked 206.274 218.792 1.06069

    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/