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 773 to 822 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Value Type
    		red
    		green
    		network_comparison
    194 aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [swissprot;acc:p29972] Squared 71346.6 95965.1 1.34505
    cyclin g2. [swissprot;acc:q16589] Measured 17738.6 13995.7 1.26743
    eap30 subunit of ell complex. [refseq;acc:nm_007241] Rooted 59.6399 51.9242 1.1486
    nuclear protein ukp68. [refseq;acc:nm_024824] Ranked 227.491 199.458 1.14055
    195 cyclin g1 (cyclin g). [swissprot;acc:p51959] Measured 17738.5 13995.6 1.26743
    huntingtin interacting protein c. [refseq;acc:nm_012272] Ranked 227.971 200.417 1.13748
    liv-1 protein, estrogen regulated. [refseq;acc:nm_012319] Rooted 59.6399 51.9242 1.1486
    translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [swissprot;acc:p51571] Squared 71062.4 95488.9 1.34373
    196 calsyntenin-1 precursor. [swissprot;acc:o94985]
    forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] Ranked 263.215 231.407 1.13745
    glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329] Rooted 59.6399 51.9242 1.1486
    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 17738.5 13995.7 1.26742
    197 forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] Ranked 263.215 231.407 1.13745
    gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747] Rooted 59.6399 51.9242 1.1486
    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 13995.7 1.26742
    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 95488.9 1.34373
    198 b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056] Measured 17710.9 13977.7 1.26708
    forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] Ranked 263.191 231.394 1.13741
    glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259] Rooted 59.6399 51.9242 1.1486
    protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [swissprot;acc:p23467] Squared 71062.2 95488.6 1.34373
    199 palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5] Ranked 242.735 276.059 1.13729
    serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323] Measured 4916.8 3888.18 1.26455
    source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] Rooted 61.2893 70.3856 1.14842
    thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7] Squared 71062.2 95488.6 1.34373
    200 crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] Measured 4808.79 6074.21 1.26315
    egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215] Ranked 242.718 276.018 1.1372
    gk001 protein. [refseq;acc:nm_020198] Squared 71062.2 95488.6 1.34373
    oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Rooted 61.2893 70.3856 1.14842
    201 calsyntenin-2 precursor. [swissprot;acc:q9h4d0] Squared 71033.4 95440.2 1.3436
    dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656] Rooted 61.2893 70.3856 1.14842
    splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] Ranked 240.133 211.382 1.13601
    t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] Measured 4810.22 6075.04 1.26294
    202 calsyntenin-3 precursor. [swissprot;acc:q9bqt9] Squared 71030.1 95434.8 1.34358
    enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511] Measured 4812.01 6076.09 1.26269
    short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] Ranked 201.478 228.784 1.13553
    splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] Rooted 57.3527 65.7973 1.14724
    203 autophagy protein 12-like (apg12-like). [swissprot;acc:o94817] Measured 11757.8 9352.11 1.25723
    ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] Ranked 201.515 228.752 1.13516
    hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] Squared 20988.2 15632.1 1.34263
    transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] Rooted 46.3291 53.1063 1.14628
    204 short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62] Ranked 201.515 228.752 1.13516
    small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] Measured 4512.19 5655.52 1.25339
    Rooted 55.8956 63.9636 1.14434
    source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] Squared 12326.4 16522.9 1.34045
    205 luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] Ranked 228.1 200.968 1.13501
    oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Squared 12326.4 16522.9 1.34045
    small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] Measured 4512.19 5655.52 1.25339
    Rooted 55.8956 63.9636 1.14434
    206 atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] Measured 5720.25 4577.5 1.24965
    dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656] Squared 12326.4 16522.9 1.34045

    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/