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 green network_comparison
    Results: HTML CSV LaTeX Showing element 2001 to 2050 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		Value Type
    		description
    		Network Comparison Type
    		red
    		green
    		network_comparison
    251 BCAR3 Measured breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] Subtracted 4579.34 5940.64 1361.3
    BCL6B Squared b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [refseq;acc:nm_181844] Divided 69165.6 52992.1 1.30521
    CDK2AP1 Rooted cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519] Subtracted 27.9136 37.2872 9.3736
    HARS Squared histidyl-trna synthetase (ec 6.1.1.21) (histidine--trna ligase) (hisrs). [swissprot;acc:p12081] 34506.3 43476 8969.7
    HCK Measured tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] Divided 6417.18 7859.6 1.22477
    MAX Rooted max protein. [swissprot;acc:p25912] 56.3054 63.7148 1.13159
    RPS20 Ranked 40s ribosomal protein s20. [swissprot;acc:p17075] Subtracted 243.5 267.21 23.71
    SLC15A1 oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] Divided 186.172 166.661 1.11707
    252 CENPJ Squared centromere protein j; centrosomal p4.1-associated protein; lyst-interacting protein lip1; lag-3-associated protein. [refseq;acc:nm_018451] Subtracted 51286.6 42334.5 8952.1
    CRKL Measured crk-like protein. [swissprot;acc:p46109] Divided 6417.18 7859.6 1.22477
    EIF4G1 Ranked eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] 237.292 212.457 1.11689
    GYS1 Measured glycogen [starch] synthase, muscle (ec 2.4.1.11). [swissprot;acc:p13807] Subtracted 9648.27 10994.9 1346.63
    MXD1 Ranked mad protein (max dimerizer). [swissprot;acc:q05195] 228 204.333 23.667
    NFYB Rooted 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] Divided 51.6736 58.4422 1.13099
    PASK Squared pas domain containing serine/threonine kinase; pas-serine/threonine kinase. [refseq;acc:nm_015148] 69165 52991.7 1.3052
    ZNF547 Rooted sedlin. [swissprot;acc:o14582] Subtracted 116.061 125.434 9.373
    253 no value Measured endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759] 9642.22 10986.4 1344.18
    Rooted synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] 116.061 125.434 9.373
    ABL1 Measured proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] Divided 6417.18 7859.59 1.22477
    BCL6 Squared b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [swissprot;acc:p41182] 69165 52991.7 1.3052
    GYS1 glycogen [starch] synthase, muscle (ec 2.4.1.11). [swissprot;acc:p13807] Subtracted 39478.8 48419 8940.2
    MXD1 Ranked mad protein (max dimerizer). [swissprot;acc:q05195] Divided 228 204.333 1.11583
    NFYB 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] Subtracted 251.679 228.037 23.642
    SRP9 Rooted signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Divided 53.5956 60.465 1.12817
    254 ESRRB Squared steroid hormone receptor err2 (estrogen-related receptor, beta) (err-beta) (estrogen receptor-like 2) (err beta-2). [swissprot;acc:o95718] Subtracted 59338.5 68268.3 8929.8
    FYN Measured proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] Divided 6417.18 7859.6 1.22477
    GYS2 glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840] Subtracted 9634.98 10976.2 1341.22
    MXI1 Ranked max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] 227.999 204.357 23.642
    SNAI2 Squared zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623] Divided 69165 52991.7 1.3052
    SRP9 Rooted signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 53.607 60.4452 1.12756
    STT3B Ranked source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] 200.691 179.88 1.11569
    TRAPPC3 Rooted bet3 homolog. [swissprot;acc:o43617] Subtracted 116.061 125.434 9.373
    255 no value Squared endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759] 39472 48393.1 8921.1
    CTBP1 c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363] Divided 69123.3 52967 1.30503
    FGR Measured proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] 6417.18 7859.6 1.22477
    MXD1 mad protein (max dimerizer). [swissprot;acc:q05195] Subtracted 4455.95 5774.03 1318.08
    MXD4 Ranked max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] 227.999 204.366 23.633
    PAPOLA Rooted poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] 132.156 122.835 9.321
    RRM2 ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] Divided 62.9007 70.8854 1.12694
    STT3A Ranked oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] 200.691 179.88 1.11569
    256 no value Squared formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] 15465.1 20151 1.303
    CEBPZ Rooted ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] 48.0045 54.0843 1.12665
    EXOC2 exocyst complex component sec5. [swissprot;acc:q96kp1] Subtracted 132.114 122.802 9.312
    GRAP2 Measured 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] Divided 6417.19 7859.51 1.22476
    GYS2 Squared glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840] Subtracted 39463.9 48362.1 8898.2
    MXI1 Measured max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] 4456.67 5773.77 1317.1
    Ranked Divided 227.999 204.357 1.11569
    RAB24 max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] Subtracted 204.37 23.629
    257 no value Squared huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] Divided 15482.3 20162.4 1.30229
    CMPK Ranked ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085] Subtracted 242.14 265.697 23.557

    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/