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 description Hugo Network Comparison Type red Value Type Interaction Map Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 2025 to 2074 of 33156 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		description
    		Hugo
    		red
    		Value Type
    		Interaction Map
    		green
    		network_comparison
    254 adp-ribosylation factor 5. [swissprot;acc:p26437] ARF5 59478 Squared Low confidence 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 8219.97 Measured 8727.87 1.06179
    nadph oxidase 3; nadph oxidase catalytic subunit-like 3. [refseq;acc:nm_015718] NOX3 210.414 Ranked 201.035 1.04665
    proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] FYN 6417.18 Measured High confidence 7859.6 1.22477
    signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] SRP9 53.607 Rooted 60.4452 1.12756
    source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] STT3B 200.691 Ranked 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 70.5903 Rooted Low confidence 74.601 1.05682
    zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623] SNAI2 69165 Squared High confidence 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 53312.7 Low confidence 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 210.413 Ranked 201.035 1.04665
    oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] STT3A 200.691 High confidence 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 67.7782 Rooted Low confidence 71.6191 1.05667
    proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] FGR 6417.18 Measured High confidence 7859.6 1.22477
    ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] RRM2 62.9007 Rooted 70.8854 1.12694
    sel-1 homolog precursor (suppressor of lin-12-like protein) (sel-1l). [swissprot;acc:q9ubv2] SEL1L 8219.95 Measured Low confidence 8727.84 1.06179
    256 ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] CEBPZ 48.0045 Rooted High confidence 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 15465.1 Squared 20151 1.303
    fructose-1,6-bisphosphatase (ec 3.1.3.11) (d-fructose-1,6-bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:p09467] FBP1 8216.87 Measured Low confidence 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 6417.19 High confidence 7859.51 1.22476
    max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] MXI1 227.999 Ranked 204.357 1.11569
    oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] STT3A 199.376 Low confidence 190.521 1.04648
    probable atp-dependent rna helicase ddx10 (dead-box protein 10). [swissprot;acc:q13206] DDX10 50792.6 Squared 46547.8 1.09119
    single-minded homolog 1. [swissprot;acc:p81133] SIM1 67.7782 Rooted 71.6191 1.05667
    257 cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] COMP 51.6125 High confidence 45.8409 1.12591
    ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] CUTL1 6417.31 Measured 7858.12 1.22452
    cln3 protein (battenin) (batten disease protein). [swissprot;acc:q13286] no value 68.3669 Rooted Low confidence 72.2396 1.05665
    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 200.691 Ranked High confidence 179.88 1.11569
    glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840] GYS2 53244.4 Squared Low confidence 48813.4 1.09077
    huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] no value 15482.3 High confidence 20162.4 1.30229
    synaptojanin 1 (ec 3.1.3.36) (synaptic inositol-1,4,5-trisphosphate 5- phosphatase 1). [swissprot;acc:o43426] SYNJ1 8082.34 Measured Low confidence 8579.93 1.06157
    tropomyosin alpha 3 chain (tropomyosin 3) (tropomyosin gamma). [swissprot;acc:p06753] TPM3 201.316 Ranked 192.404 1.04632
    258 adp-ribosylation factor guanine nucleotide factor 6; hepatocellular carcinoma-associated antigen 67. [refseq;acc:nm_015310] PSD3 50448.8 Squared 46264.1 1.09045
    aflatoxin b1 aldehyde reductase 2 (ec 1.-.-.-) (afb1-ar 2). [swissprot;acc:o95154] AKR7A3 9249.74 Measured 9818.95 1.06154
    homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] CUTL2 6417.33 High confidence 7857.93 1.22449
    huntingtin interacting protein 1 (hip-i). [swissprot;acc:o00291] HIP1 76438 Squared 58889.7 1.29799
    max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] MXD4 227.999 Ranked 204.366 1.11564
    thrombospondin 3 precursor. [swissprot;acc:p49746] THBS3 51.6132 Rooted 45.8422 1.12589
    tropomyosin 1 alpha chain (alpha-tropomyosin). [swissprot;acc:p09493] TPM1 201.304 Ranked Low confidence 192.427 1.04613
    ubiquitin-conjugating enzyme e2 g1 (ec 6.3.2.19) (ubiquitin-protein ligase g1) (ubiquitin carrier protein g1) (e217k) (ubc7). [swissprot;acc:q99462] UBE2G1 70.3765 Rooted 74.3627 1.05664
    259 goodpasture antigen-binding protein (ec 2.7.1.37) (gpbp) (collagen type iv alpha 3 binding protein) (star-related lipid transfer protein 11) (stard11) (start domain-containing protein 11). [swissprot;acc:q9y5p4] COL4A3BP 76360.8 Squared High confidence 58841.7 1.29773
    max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] RAB24 227.999 Ranked 204.37 1.11562
    neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] WASL 6417.81 Measured 7852.52 1.22355
    oligophrenin 1. [swissprot;acc:o60890] OPHN1 6428.7 Low confidence 6824.22 1.06152
    parafibromin. [refseq;acc:nm_024529] CDC73 67.6012 Rooted 71.4286 1.05662
    trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317] PDSS1 211.794 Ranked 202.482 1.04599
    trs85 homolog. [swissprot;acc:q9y2l5] KIAA1012 50448.8 Squared 46264.1 1.09045
    tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] TFIP11 58.2964 Rooted High confidence 65.5926 1.12516
    260 aflatoxin b1 aldehyde reductase 1 (ec 1.-.-.-) (afb1-ar 1) (aldoketoreductase 7). [swissprot;acc:o43488] AKR7A2 9246.23 Measured Low confidence 9814.59 1.06147
    ankyrin repeat domain protein 7 (testis-specific protein tsa806). [swissprot;acc:q92527] ANKRD7 216.855 Ranked 207.34 1.04589

    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/