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 Value Type Network Comparison Type Interaction Map red Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 2001 to 2050 of 33156 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Value Type
    		Interaction Map
    		red
    		green
    		network_comparison
    251 b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [refseq;acc:nm_181844] BCL6B Squared High confidence 69165.6 52992.1 1.30521
    eferin. [swissprot;acc:o75154] RAB11FIP3 Low confidence 34469.6 37645.4 1.09213
    kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] KYNU Measured 8527.55 9058.09 1.06221
    max protein. [swissprot;acc:p25912] MAX Rooted High confidence 56.3054 63.7148 1.13159
    nadph oxidase, ef hand calcium-binding domain 5. [refseq;acc:nm_024505] NOX5 Ranked Low confidence 210.415 201.035 1.04666
    oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] SLC15A1 High confidence 186.172 166.661 1.11707
    septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] SEPT7 Rooted Low confidence 90.452 95.6145 1.05707
    tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] HCK Measured High confidence 6417.18 7859.6 1.22477
    252 1-acyl-sn-glycerol-3-phosphate acyltransferase gamma (ec 2.3.1.51) (1- agp acyltransferase 3) (1-agpat 3) (lysophosphatidic acid acyltransferase-gamma) (lpaat-gamma) (1-acylglycerol-3-phosphate o- acyltransferase 3). [swissprot;acc:q9nrz7] AGPAT3 Low confidence 8492.92 9018.94 1.06194
    crk-like protein. [swissprot;acc:p46109] CRKL High confidence 6417.18 7859.6 1.22477
    cytochrome b-245 heavy chain (p22 phagocyte b-cytochrome) (neutrophil cytochrome b, 91 kda polypeptide) (cgd91-phox) (gp91-phox) (heme binding membrane glycoprotein gp91phox) (cytochrome b(558) beta chain) (superoxide-generating nadph oxidase heavy chain subunit). [swissprot;acc:p04839] CYBB Ranked Low confidence 210.414 201.035 1.04665
    eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] EIF4G1 High confidence 237.292 212.457 1.11689
    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 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
    ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] RRAGA Rooted Low confidence 86.7994 91.752 1.05706
    ras-related protein r-ras (p23). [swissprot;acc:p10301] RRAS Squared 50409.8 46187.4 1.09142
    253 b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [swissprot;acc:p41182] BCL6 High confidence 69165 52991.7 1.3052
    calcium-transporting atpase type 2c, member 1 (ec 3.6.3.8) (atpase 2c1) (atp-dependent ca(2+) pump pmr1) (hussy-28). [swissprot;acc:p98194] ATP2C1 Rooted Low confidence 66.0401 69.8058 1.05702
    fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] FBP2 Measured 8223.39 8732.25 1.06188
    mad protein (max dimerizer). [swissprot;acc:q05195] MXD1 Ranked High confidence 228 204.333 1.11583
    nadph oxidase 4. [refseq;acc:nm_016931] NOX4 Low confidence 210.413 201.035 1.04665
    proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] ABL1 Measured High confidence 6417.18 7859.59 1.22477
    ras-related protein r-ras2 (ras-like protein tc21) (teratocarcinoma oncogene). [swissprot;acc:p17082] RRAS2 Squared Low confidence 50402.7 46184.6 1.09133
    signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] SRP9 Rooted High confidence 53.5956 60.465 1.12817
    254 adp-ribosylation factor 5. [swissprot;acc:p26437] ARF5 Squared Low confidence 59478 54500.5 1.09133
    dj842g6.2 (novel protein imilar to sel1l (sel-1 (suppressor of lin-12, c.elegans)-like)) (fragment). [sptrembl;acc:q9ugd3] SEL1L2 Measured 8219.97 8727.87 1.06179
    nadph oxidase 3; nadph oxidase catalytic subunit-like 3. [refseq;acc:nm_015718] NOX3 Ranked 210.414 201.035 1.04665
    proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] FYN Measured High confidence 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
    splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435] SF3B2 Rooted Low confidence 70.5903 74.601 1.05682
    zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623] SNAI2 Squared High confidence 69165 52991.7 1.3052
    255 c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363] CTBP1 69123.3 52967 1.30503
    glycogen [starch] synthase, muscle (ec 2.4.1.11). [swissprot;acc:p13807] GYS1 Low confidence 53312.7 48853.1 1.09129
    nadph oxidase homolog 1 (nox-1) (noh-1) (nadh/nadph mitogenic oxidase subunit p65-mox) (mitogenic oxidase 1) (mox1). [swissprot;acc:q9y5s8] NOX1 Ranked 210.413 201.035 1.04665
    oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] STT3A High confidence 200.691 179.88 1.11569
    peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [swissprot;acc:o14936] CASK Rooted Low confidence 67.7782 71.6191 1.05667
    proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] FGR Measured High confidence 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
    sel-1 homolog precursor (suppressor of lin-12-like protein) (sel-1l). [swissprot;acc:q9ubv2] SEL1L Measured Low confidence 8219.95 8727.84 1.06179
    256 ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] CEBPZ Rooted High confidence 48.0045 54.0843 1.12665
    formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] no value Squared 15465.1 20151 1.303
    fructose-1,6-bisphosphatase (ec 3.1.3.11) (d-fructose-1,6-bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:p09467] FBP1 Measured Low confidence 8216.87 8723.91 1.06171
    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 High confidence 6417.19 7859.51 1.22476
    max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] MXI1 Ranked 227.999 204.357 1.11569
    oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] STT3A Low confidence 199.376 190.521 1.04648
    probable atp-dependent rna helicase ddx10 (dead-box protein 10). [swissprot;acc:q13206] DDX10 Squared 50792.6 46547.8 1.09119
    single-minded homolog 1. [swissprot;acc:p81133] SIM1 Rooted 67.7782 71.6191 1.05667
    257 cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] COMP High confidence 51.6125 45.8409 1.12591
    ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] CUTL1 Measured 6417.31 7858.12 1.22452

    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/