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 Value Type description Network Comparison Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 775 to 824 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		Value Type
    		description
    		red
    		network_comparison
    		green
    194 SNF8 Rooted eap30 subunit of ell complex. [refseq;acc:nm_007241] 59.6399 1.1486 51.9242
    ZC3H14 Ranked nuclear protein ukp68. [refseq;acc:nm_024824] 227.491 1.14055 199.458
    195 CCNG1 Measured cyclin g1 (cyclin g). [swissprot;acc:p51959] 17738.5 1.26743 13995.6
    PRPF40B Ranked huntingtin interacting protein c. [refseq;acc:nm_012272] 227.971 1.13748 200.417
    SLC39A6 Rooted liv-1 protein, estrogen regulated. [refseq;acc:nm_012319] 59.6399 1.1486 51.9242
    SSR4 Squared translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [swissprot;acc:p51571] 71062.4 1.34373 95488.9
    196 CLSTN1 calsyntenin-1 precursor. [swissprot;acc:o94985]
    FOXP4 Ranked forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] 263.215 1.13745 231.407
    GAD2 Rooted glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329] 59.6399 1.1486 51.9242
    PPP2R5E Measured 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] 17738.5 1.26742 13995.7
    197 no value Squared 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] 71062.4 1.34373 95488.9
    FOXP1 Ranked forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] 263.215 1.13745 231.407
    NAPG Rooted gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747] 59.6399 1.1486 51.9242
    PPP2R5A Measured 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] 17738.5 1.26742 13995.7
    198 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] 17710.9 1.26708 13977.7
    FOXP3 Ranked forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] 263.191 1.13741 231.394
    GAD1 Rooted glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259] 59.6399 1.1486 51.9242
    PTPRB Squared protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [swissprot;acc:p23467] 71062.2 1.34373 95488.6
    199 EGFL8 Ranked palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5] 242.735 1.13729 276.059
    PPP2CA Measured serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323] 4916.8 1.26455 3888.18
    PRSS16 Squared thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7] 71062.2 1.34373 95488.6
    STT3B Rooted source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] 61.2893 1.14842 70.3856
    200 BCAR1 Measured crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] 4808.79 1.26315 6074.21
    CCDC47 Squared gk001 protein. [refseq;acc:nm_020198] 71062.2 1.34373 95488.6
    EGFL7 Ranked egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215] 242.718 1.1372 276.018
    STT3A Rooted oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] 61.2893 1.14842 70.3856
    201 CCT4 Measured t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] 4810.22 1.26294 6075.04
    CLSTN2 Squared calsyntenin-2 precursor. [swissprot;acc:q9h4d0] 71033.4 1.3436 95440.2
    DDOST Rooted 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] 61.2893 1.14842 70.3856
    SF4 Ranked splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] 240.133 1.13601 211.382
    202 no value Rooted splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] 57.3527 1.14724 65.7973
    CLSTN3 Squared calsyntenin-3 precursor. [swissprot;acc:q9bqt9] 71030.1 1.34358 95434.8
    NEDD9 Measured 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] 4812.01 1.26269 6076.09
    TRPC4 Ranked short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] 201.478 1.13553 228.784
    203 no value Squared hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] 20988.2 1.34263 15632.1
    Rooted transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] 46.3291 1.14628 53.1063
    ATG12 Measured autophagy protein 12-like (apg12-like). [swissprot;acc:o94817] 11757.8 1.25723 9352.11
    TBC1D10A Ranked ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] 201.515 1.13516 228.752
    204 no value Measured small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] 4512.19 1.25339 5655.52
    Rooted 55.8956 1.14434 63.9636
    STT3B Squared source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] 12326.4 1.34045 16522.9
    TRPC5 Ranked short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62] 201.515 1.13516 228.752
    205 LUC7L2 luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] 228.1 1.13501 200.968
    SNRPF Measured small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] 4512.19 1.25339 5655.52
    Rooted 55.8956 1.14434 63.9636
    STT3A Squared oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] 12326.4 1.34045 16522.9
    206 no value Measured atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] 5720.25 1.24965 4577.5
    Rooted gaba-a receptor-associated protein. [sptrembl;acc:q9by60] 140.508 1.14348 122.878
    DDOST Squared 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] 12326.4 1.34045 16522.9
    LUC7L Ranked luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] 228.085 1.13472 201.006

    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/