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 Value Type Hugo description Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 980 to 1029 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Value Type
    		Hugo
    		description
    		red
    		green
    		network_comparison
    245 Rooted MYO5C myosin vc (myosin 5c). [swissprot;acc:q9nqx4] 146.94 167.046 1.13683
    246 Measured HOMER3 homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] 4252.66 5213.05 1.22583
    Ranked EIF4G3 eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] 237.312 212.363 1.11748
    Squared PYGB glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] 8875.01 6768.05 1.31131
    Rooted no value myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] 146.94 167.046 1.13683
    247 Measured WAS wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] 6416.68 7865.15 1.22574
    Ranked no value rna-binding protein. [refseq;acc:nm_019027] 237.302 212.41 1.11719
    Squared PYGL glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] 8875.01 6768.05 1.31131
    Rooted DDX56 probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] 47.3621 53.8355 1.13668
    248 Measured CRK proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] 6417.18 7859.6 1.22477
    Ranked no value apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] 237.302 212.41 1.11719
    Squared MYO15A myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] 8875.01 6768.05 1.31131
    Rooted LSM5 u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] 56.0466 63.4808 1.13264
    249 Measured ABL2 tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] 6417.18 7859.59 1.22477
    Ranked SYNCRIP ns1-associated protein 1. [refseq;acc:nm_006372] 237.302 212.41 1.11719
    Squared PYGM glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] 8875.01 6768.05 1.31131
    Rooted BRF1 transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [swissprot;acc:q92994] 55.5965 62.9349 1.13199
    250 Measured no value proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] 6417.18 7859.6 1.22477
    Ranked HNRNPR heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] 237.302 212.41 1.11719
    Squared CTBP2 c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545] 69201.8 53013.4 1.30536
    Rooted NOLA1 nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] 55.5965 62.9349 1.13199
    251 Measured HCK tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] 6417.18 7859.6 1.22477
    Ranked SLC15A1 oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] 186.172 166.661 1.11707
    Squared BCL6B b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [refseq;acc:nm_181844] 69165.6 52992.1 1.30521
    Rooted MAX max protein. [swissprot;acc:p25912] 56.3054 63.7148 1.13159
    252 Measured CRKL crk-like protein. [swissprot;acc:p46109] 6417.18 7859.6 1.22477
    Ranked EIF4G1 eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] 237.292 212.457 1.11689
    Squared PASK pas domain containing serine/threonine kinase; pas-serine/threonine kinase. [refseq;acc:nm_015148] 69165 52991.7 1.3052
    Rooted 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] 51.6736 58.4422 1.13099
    253 Measured ABL1 proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] 6417.18 7859.59 1.22477
    Ranked MXD1 mad protein (max dimerizer). [swissprot;acc:q05195] 228 204.333 1.11583
    Squared BCL6 b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [swissprot;acc:p41182] 69165 52991.7 1.3052
    Rooted SRP9 signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 53.5956 60.465 1.12817
    254 Measured FYN proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] 6417.18 7859.6 1.22477
    Ranked STT3B source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] 200.691 179.88 1.11569
    Squared SNAI2 zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623] 69165 52991.7 1.3052
    Rooted SRP9 signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 53.607 60.4452 1.12756
    255 Measured FGR proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] 6417.18 7859.6 1.22477
    Ranked STT3A oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] 200.691 179.88 1.11569
    Squared CTBP1 c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363] 69123.3 52967 1.30503
    Rooted RRM2 ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] 62.9007 70.8854 1.12694
    256 Measured GRAP2 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] 6417.19 7859.51 1.22476
    Ranked MXI1 max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] 227.999 204.357 1.11569
    Squared no value 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
    Rooted CEBPZ ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] 48.0045 54.0843 1.12665
    257 Measured CUTL1 ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] 6417.31 7858.12 1.22452
    Ranked 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] 200.691 179.88 1.11569
    Squared no value huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] 15482.3 20162.4 1.30229
    Rooted COMP cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] 51.6125 45.8409 1.12591
    258 Measured CUTL2 homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] 6417.33 7857.93 1.22449

    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/