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 Value Type Network Comparison Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 1551 to 1600 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		Network Comparison Type
    		red
    		network_comparison
    		green
    194 SNF8 eap30 subunit of ell complex. [refseq;acc:nm_007241] Rooted Divided 59.6399 1.1486 51.9242
    ZC3H14 nuclear protein ukp68. [refseq;acc:nm_024824] Ranked 227.491 1.14055 199.458
    195 CCNG1 cyclin g1 (cyclin g). [swissprot;acc:p51959] Measured 17738.5 1.26743 13995.6
    Rooted Subtracted 116.707 10.663 106.044
    CHRNA6 neuronal acetylcholine receptor protein, alpha-6 chain precursor. [swissprot;acc:q15825] Squared 42411.6 13390.5 55802.1
    PCYT1B cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3] Ranked 241.373 25.979 267.352
    PRPF40B huntingtin interacting protein c. [refseq;acc:nm_012272] Divided 227.971 1.13748 200.417
    SLC39A6 liv-1 protein, estrogen regulated. [refseq;acc:nm_012319] Rooted 59.6399 1.1486 51.9242
    SSR4 translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [swissprot;acc:p51571] Squared 71062.4 1.34373 95488.9
    UFC1 protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] Measured Subtracted 3074.57 1492.94 4567.51
    196 no value hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] Ranked 272.781 25.889 246.892
    AQP4 aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [swissprot;acc:p55087] Measured 10640.2 1477.6 12117.8
    CLSTN1 calsyntenin-1 precursor. [swissprot;acc:o94985] Squared Divided 71062.4 1.34373 95488.9
    FOXP4 forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] Ranked 263.215 1.13745 231.407
    GAD2 glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329] Rooted 59.6399 1.1486 51.9242
    ISCU nitrogen fixation cluster-like. [refseq;acc:nm_014301] Squared Subtracted 42411.6 13390.5 55802.1
    PPP2R5A serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, alpha isoform (pp2a, b subunit, b' alpha isoform) (pp2a, b subunit, b56 alpha isoform) (pp2a, b subunit, pr61 alpha isoform) (pp2a, b subunit, r5 alpha isoform). [swissprot;acc:q15172] Rooted 116.707 10.663 106.044
    PPP2R5E serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, epsilon isoform (pp2a, b subunit, b' epsilon isoform) (pp2a, b subunit, b56 epsilon isoform) (pp2a, b subunit, pr61 epsilon isoform) (pp2a, b subunit, r5 epsilon isoform). [swissprot;acc:q16537] Measured Divided 17738.5 1.26742 13995.7
    197 no value succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [swissprot;acc:o14521] Squared 71062.4 1.34373 95488.9
    AQP5 aquaporin 5. [swissprot;acc:p55064] Measured Subtracted 10640 1477.6 12117.6
    FOXP1 forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] Ranked Divided 263.215 1.13745 231.407
    LUC7L2 luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] Rooted Subtracted 55.2859 10.6429 65.9288
    NAPG gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747] Divided 59.6399 1.1486 51.9242
    PPP2R5A serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, alpha isoform (pp2a, b subunit, b' alpha isoform) (pp2a, b subunit, b56 alpha isoform) (pp2a, b subunit, pr61 alpha isoform) (pp2a, b subunit, r5 alpha isoform). [swissprot;acc:q15172] Measured 17738.5 1.26742 13995.7
    SNORA7A 60s ribosomal protein l32. [swissprot;acc:p02433] Ranked Subtracted 241.13 25.839 266.969
    STARD13 star-related lipid transfer protein 13 (stard13) (start domain- containing protein 13) (46h23.2). [swissprot;acc:q9y3m8] Squared 42411.6 13390.5 55802.1
    198 no value 40s ribosomal protein s29. [swissprot;acc:p30054] Ranked 241.849 25.793 267.642
    AQP2 aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181] Measured 10639.9 1477.5 12117.4
    BRAF b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056] Divided 17710.9 1.26708 13977.7
    Rooted Subtracted 116.576 10.628 105.948
    FOXP3 forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] Ranked Divided 263.191 1.13741 231.394
    GAD1 glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259] Rooted 59.6399 1.1486 51.9242
    PTPRB protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [swissprot;acc:p23467] Squared 71062.2 1.34373 95488.6
    STARD8 star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [swissprot;acc:q92502] Subtracted 42411.6 13390.5 55802.1
    199 CHRNA2 neuronal acetylcholine receptor protein, alpha-2 chain precursor. [swissprot;acc:q15822]
    EGFL8 palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5] Ranked Divided 242.735 1.13729 276.059
    LUC7L luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] Rooted Subtracted 55.297 10.6266 65.9236
    MIP lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [swissprot;acc:p30301] Measured 10639.8 1477.5 12117.3
    PPP2CA serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323] Divided 4916.8 1.26455 3888.18
    PRSS16 thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7] Squared 71062.2 1.34373 95488.6
    RPS11 40s ribosomal protein s11. [swissprot;acc:p04643] Ranked Subtracted 241.399 25.689 267.088
    STT3B source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] Rooted Divided 61.2893 1.14842 70.3856
    200 no value 60s ribosomal protein l17 (l23). [swissprot;acc:p18621] Ranked Subtracted 241.808 25.527 267.335
    AQP1 aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [swissprot;acc:p29972] Measured 10635.3 1476.1 12111.4
    BCAR1 crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] Divided 4808.79 1.26315 6074.21
    CCDC47 gk001 protein. [refseq;acc:nm_020198] Squared 71062.2 1.34373 95488.6
    EGFL7 egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215] Ranked 242.718 1.1372 276.018
    MAPKAPK3 mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635] Squared Subtracted 42411.6 13390.5 55802.1
    PPP2CA serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323] Rooted 63.5827 10.4971 53.0856
    STT3A oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Divided 61.2893 1.14842 70.3856

    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/