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 green network_comparison
    Results: HTML CSV LaTeX Showing element 2380 to 2429 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Value Type
    		red
    		green
    		network_comparison
    595 vav proto-oncogene. [swissprot;acc:p15498] VAV1 Ranked 212.2 199.849 1.0618
    596 5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619] PRKAG1 Squared 34129.6 40434.5 1.18473
    cbf1 interacting corepressor. [refseq;acc:nm_004882] no value Rooted 60.0587 65.0057 1.08237
    histone h2b.s (h2b/s). [swissprot;acc:p57053] Measured 3946.32 4475.47 1.13409
    vav-3 protein. [swissprot;acc:q9ukw4] VAV3 Ranked 212.253 199.908 1.06175
    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 40434.2 1.18473
    evolutionarily conserved g-patch domain containing. [refseq;acc:nm_018025] GPATCH1 Rooted 60.0587 65.0057 1.08237
    histone h2b.d (h2b/d). [swissprot;acc:q99877] no value Measured 3946.32 4475.47 1.13409
    vav-2 protein. [swissprot;acc:p52735] VAV2 Ranked 212.526 200.212 1.0615
    598 5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741] PRKAB2 Squared 34129.6 40434.5 1.18473
    histone h3.4 (h3t) (h3/t) (h3/g). [swissprot;acc:q16695] HIST3H3 Measured 3946.32 4475.47 1.13409
    methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192] MARS Rooted 61.2527 66.2644 1.08182
    rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [swissprot;acc:p31749] AKT1 Ranked 248.463 234.095 1.06138
    599 5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9] PRKAG3 Squared 34129.6 40434.5 1.18473
    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 138.375 127.926 1.08168
    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 248.463 234.095 1.06138
    testis-specific histone h2b; h2b histone family, member u, (testis-specific). [refseq;acc:nm_170610] HIST1H2BA Measured 3946.32 4475.47 1.13409
    600 5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478] PRKAB1 Squared 34129.6 40434.5 1.18473
    histone h2b.e (h2b/e). [swissprot;acc:q99879] no value Measured 3946.32 4475.47 1.13409
    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 248.463 234.095 1.06138
    trs85 homolog. [swissprot;acc:q9y2l5] KIAA1012 Rooted 138.375 127.926 1.08168
    601 5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0] PRKAG2 Squared 34129.6 40434.5 1.18473
    symplekin. [swissprot;acc:q92797] SYMPK Measured 15213.4 13418.1 1.1338
    vam6/vps39-like protein (hvam6p). [swissprot;acc:q96jc1] VPS39 Ranked 206.274 218.792 1.06069
    wd-repeat protein wdc146. [swissprot;acc:q9c0j8] WDR33 Rooted 138.032 127.651 1.08132
    602 ataxin 2 related protein isoform a; ataxin-2 domain protein. [refseq;acc:nm_007245] ATXN2L Measured 4864.66 5514.87 1.13366
    cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] CPSF1 Rooted 138.032 127.651 1.08132
    microtubule-associated protein 4 (map 4). [swissprot;acc:p27816] MAP4 Ranked 206.274 218.792 1.06069
    spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] TXNL4A Squared 19129.8 22652.9 1.18417
    603 ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] no value Measured 4864.66 5514.87 1.13366
    lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [swissprot;acc:q9uju2] LEF1 Ranked 225.829 212.945 1.0605
    nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594] no value Squared 34071.5 40336.5 1.18388
    u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695] Rooted 60.0742 64.9418 1.08103
    604 60s ribosomal protein l15. [swissprot;acc:p39030] RPL15 Ranked 217.862 230.978 1.0602
    alpha-nac protein. [sptrembl;acc:q9h009] no value Squared 34069.4 40333 1.18385
    step ii splicing factor slu7. [refseq;acc:nm_006425] SLU7 Rooted 60.0742 64.9418 1.08103
    vinculin (metavinculin). [swissprot;acc:p18206] VCL Measured 5958.23 6743.37 1.13177
    605 histone h2b.c (h2b/c). [swissprot;acc:q99880] HIST1H2BL Ranked 247.47 233.441 1.0601
    probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] ATP2C2 Measured 6143.52 6950.75 1.1314
    sedlin. [swissprot;acc:o14582] ZNF547 Rooted 116.061 125.434 1.08076
    small gtp-binding tumor suppressor 1. [refseq;acc:nm_145173] DIRAS1 Squared 34068.1 40330.8 1.18383
    606 calcium-transporting atpase type 2c, member 1 (ec 3.6.3.8) (atpase 2c1) (atp-dependent ca(2+) pump pmr1) (hussy-28). [swissprot;acc:p98194] ATP2C1 Measured 6148.94 6955.76 1.13121
    di-ras2. [refseq;acc:nm_017594] DIRAS2 Squared 34068 40330.7 1.18383
    histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778] HIST2H2BA Ranked 247.47 233.441 1.0601
    synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] no value Rooted 116.061 125.434 1.08076
    607 bet3 homolog. [swissprot;acc:o43617] TRAPPC3
    cytosolic nonspecific dipeptidase (glutamate carboxypeptidase-like protein 1). [swissprot;acc:q96kp4] CNDP2 Squared 26583.8 31468.6 1.18375
    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 Ranked 247.47 233.441 1.0601
    likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235] CSTF2T Measured 14976.4 13246.6 1.13058
    608 histone h2b. [refseq;acc:nm_175055] no value Ranked 247.47 233.441 1.0601

    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/