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 [...,...].
    Gene Rank Hugo Network Comparison Type description Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2012 to 2061 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		Network Comparison Type
    		description
    		Value Type
    		red
    		green
    		network_comparison
    252 GYS1 Subtracted glycogen [starch] synthase, muscle (ec 2.4.1.11). [swissprot;acc:p13807] Measured 9648.27 10994.9 1346.63
    MXD1 mad protein (max dimerizer). [swissprot;acc:q05195] Ranked 228 204.333 23.667
    NFYB Divided nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [swissprot;acc:p25208] Rooted 51.6736 58.4422 1.13099
    PASK pas domain containing serine/threonine kinase; pas-serine/threonine kinase. [refseq;acc:nm_015148] Squared 69165 52991.7 1.3052
    ZNF547 Subtracted sedlin. [swissprot;acc:o14582] Rooted 116.061 125.434 9.373
    253 no value endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759] Measured 9642.22 10986.4 1344.18
    synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] Rooted 116.061 125.434 9.373
    ABL1 Divided proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] Measured 6417.18 7859.59 1.22477
    BCL6 b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [swissprot;acc:p41182] Squared 69165 52991.7 1.3052
    GYS1 Subtracted glycogen [starch] synthase, muscle (ec 2.4.1.11). [swissprot;acc:p13807] 39478.8 48419 8940.2
    MXD1 Divided mad protein (max dimerizer). [swissprot;acc:q05195] Ranked 228 204.333 1.11583
    NFYB Subtracted nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [swissprot;acc:p25208] 251.679 228.037 23.642
    SRP9 Divided signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Rooted 53.5956 60.465 1.12817
    254 ESRRB Subtracted steroid hormone receptor err2 (estrogen-related receptor, beta) (err-beta) (estrogen receptor-like 2) (err beta-2). [swissprot;acc:o95718] Squared 59338.5 68268.3 8929.8
    FYN Divided proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] Measured 6417.18 7859.6 1.22477
    GYS2 Subtracted glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840] 9634.98 10976.2 1341.22
    MXI1 max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] Ranked 227.999 204.357 23.642
    SNAI2 Divided zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623] Squared 69165 52991.7 1.3052
    SRP9 signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Rooted 53.607 60.4452 1.12756
    STT3B source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] Ranked 200.691 179.88 1.11569
    TRAPPC3 Subtracted bet3 homolog. [swissprot;acc:o43617] Rooted 116.061 125.434 9.373
    255 no value endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759] Squared 39472 48393.1 8921.1
    CTBP1 Divided c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363] 69123.3 52967 1.30503
    FGR proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] Measured 6417.18 7859.6 1.22477
    MXD1 Subtracted mad protein (max dimerizer). [swissprot;acc:q05195] 4455.95 5774.03 1318.08
    MXD4 max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] Ranked 227.999 204.366 23.633
    PAPOLA poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] Rooted 132.156 122.835 9.321
    RRM2 Divided ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] 62.9007 70.8854 1.12694
    STT3A oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Ranked 200.691 179.88 1.11569
    256 no value formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] Squared 15465.1 20151 1.303
    CEBPZ ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] Rooted 48.0045 54.0843 1.12665
    EXOC2 Subtracted exocyst complex component sec5. [swissprot;acc:q96kp1] 132.114 122.802 9.312
    GRAP2 Divided grb2-related adaptor protein 2 (gads protein) (growth factor receptor binding protein) (grblg) (grf40 adaptor protein) (grf-40) (grb-2-like protein) (grb2l) (grbx) (p38) (hematopoietic cell-associated adaptor protein grpl) (adapter protein grid) (sh3-sh2-sh3 adaptor mona). [swissprot;acc:o75791] Measured 6417.19 7859.51 1.22476
    GYS2 Subtracted glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840] Squared 39463.9 48362.1 8898.2
    MXI1 Divided max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] Ranked 227.999 204.357 1.11569
    Subtracted Measured 4456.67 5773.77 1317.1
    RAB24 max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] Ranked 227.999 204.37 23.629
    257 no value Divided huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] Squared 15482.3 20162.4 1.30229
    CMPK Subtracted ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085] Ranked 242.14 265.697 23.557
    COMP Divided cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] Rooted 51.6125 45.8409 1.12591
    CPSF3 Subtracted cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] 132.467 123.158 9.309
    CUTL1 Divided ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] Measured 6417.31 7858.12 1.22452
    DDOST 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] Ranked 200.691 179.88 1.11569
    MXD4 Subtracted max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] Measured 4456.93 5773.67 1316.74
    NME2P1 putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361] Squared 33526 42390.2 8864.2
    258 AK3 gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7] Ranked 242.14 265.697 23.557
    CUTL2 Divided homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] Measured 6417.33 7857.93 1.22449
    HIP1 huntingtin interacting protein 1 (hip-i). [swissprot;acc:o00291] Squared 76438 58889.7 1.29799
    MXD4 max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] Ranked 227.999 204.366 1.11564
    NME2 Subtracted nucleoside diphosphate kinase a (ec 2.7.4.6) (ndk a) (ndp kinase a) (tumor metastatic process-associated protein) (metastasis inhibition factor nm23) (nm23-h1). [swissprot;acc:p15531] Squared 33522.8 42384.8 8862

    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/