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 2008 to 2057 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Network Comparison Type
    		Value Type
    		red
    		green
    		network_comparison
    251 tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] HCK Divided Measured 6417.18 7859.6 1.22477
    252 centromere protein j; centrosomal p4.1-associated protein; lyst-interacting protein lip1; lag-3-associated protein. [refseq;acc:nm_018451] CENPJ Subtracted Squared 51286.6 42334.5 8952.1
    crk-like protein. [swissprot;acc:p46109] CRKL Divided Measured 6417.18 7859.6 1.22477
    eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] EIF4G1 Ranked 237.292 212.457 1.11689
    glycogen [starch] synthase, muscle (ec 2.4.1.11). [swissprot;acc:p13807] GYS1 Subtracted Measured 9648.27 10994.9 1346.63
    mad protein (max dimerizer). [swissprot;acc:q05195] MXD1 Ranked 228 204.333 23.667
    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] NFYB Divided Rooted 51.6736 58.4422 1.13099
    pas domain containing serine/threonine kinase; pas-serine/threonine kinase. [refseq;acc:nm_015148] PASK Squared 69165 52991.7 1.3052
    sedlin. [swissprot;acc:o14582] ZNF547 Subtracted Rooted 116.061 125.434 9.373
    253 b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [swissprot;acc:p41182] BCL6 Divided Squared 69165 52991.7 1.3052
    endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759] no value Subtracted Measured 9642.22 10986.4 1344.18
    glycogen [starch] synthase, muscle (ec 2.4.1.11). [swissprot;acc:p13807] GYS1 Squared 39478.8 48419 8940.2
    mad protein (max dimerizer). [swissprot;acc:q05195] MXD1 Divided Ranked 228 204.333 1.11583
    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] NFYB Subtracted 251.679 228.037 23.642
    proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] ABL1 Divided Measured 6417.18 7859.59 1.22477
    signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] SRP9 Rooted 53.5956 60.465 1.12817
    synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] no value Subtracted 116.061 125.434 9.373
    254 bet3 homolog. [swissprot;acc:o43617] TRAPPC3
    glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840] GYS2 Measured 9634.98 10976.2 1341.22
    max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] MXI1 Ranked 227.999 204.357 23.642
    proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] FYN Divided Measured 6417.18 7859.6 1.22477
    signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] SRP9 Rooted 53.607 60.4452 1.12756
    source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] STT3B Ranked 200.691 179.88 1.11569
    steroid hormone receptor err2 (estrogen-related receptor, beta) (err-beta) (estrogen receptor-like 2) (err beta-2). [swissprot;acc:o95718] ESRRB Subtracted Squared 59338.5 68268.3 8929.8
    zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623] SNAI2 Divided 69165 52991.7 1.3052
    255 c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363] CTBP1 69123.3 52967 1.30503
    endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759] no value Subtracted 39472 48393.1 8921.1
    mad protein (max dimerizer). [swissprot;acc:q05195] MXD1 Measured 4455.95 5774.03 1318.08
    max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] MXD4 Ranked 227.999 204.366 23.633
    oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] STT3A Divided 200.691 179.88 1.11569
    poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] PAPOLA Subtracted Rooted 132.156 122.835 9.321
    proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] FGR Divided Measured 6417.18 7859.6 1.22477
    ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] RRM2 Rooted 62.9007 70.8854 1.12694
    256 ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] CEBPZ 48.0045 54.0843 1.12665
    exocyst complex component sec5. [swissprot;acc:q96kp1] EXOC2 Subtracted 132.114 122.802 9.312
    formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] no value Divided Squared 15465.1 20151 1.303
    glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840] GYS2 Subtracted 39463.9 48362.1 8898.2
    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] GRAP2 Divided Measured 6417.19 7859.51 1.22476
    max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] RAB24 Subtracted Ranked 227.999 204.37 23.629
    max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] MXI1 Divided 204.357 1.11569
    Subtracted Measured 4456.67 5773.77 1317.1
    257 cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] COMP Divided Rooted 51.6125 45.8409 1.12591
    ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] CUTL1 Measured 6417.31 7858.12 1.22452
    cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] CPSF3 Subtracted Rooted 132.467 123.158 9.309
    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] DDOST Divided Ranked 200.691 179.88 1.11569
    huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] no value Squared 15482.3 20162.4 1.30229
    max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] MXD4 Subtracted Measured 4456.93 5773.67 1316.74
    putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361] NME2P1 Squared 33526 42390.2 8864.2
    ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085] CMPK Ranked 242.14 265.697 23.557
    258 gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7] AK3

    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/