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 [...,...].
    Network Comparison Type Rank Gene Value Type description Interaction Map Hugo network_comparison Filtered red green
    Results: HTML CSV LaTeX Showing element 2032 to 2081 of 66312 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Value Type
    		description
    		Interaction Map
    		Hugo
    		network_comparison
    		red
    		green
    254 Rooted splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435] Low confidence SF3B2 1.05682 70.5903 74.601
    255 Measured proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] High confidence FGR 1.22477 6417.18 7859.6
    sel-1 homolog precursor (suppressor of lin-12-like protein) (sel-1l). [swissprot;acc:q9ubv2] Low confidence SEL1L 1.06179 8219.95 8727.84
    Ranked nadph oxidase homolog 1 (nox-1) (noh-1) (nadh/nadph mitogenic oxidase subunit p65-mox) (mitogenic oxidase 1) (mox1). [swissprot;acc:q9y5s8] NOX1 1.04665 210.413 201.035
    oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] High confidence STT3A 1.11569 200.691 179.88
    Squared c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363] CTBP1 1.30503 69123.3 52967
    glycogen [starch] synthase, muscle (ec 2.4.1.11). [swissprot;acc:p13807] Low confidence GYS1 1.09129 53312.7 48853.1
    Rooted peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [swissprot;acc:o14936] CASK 1.05667 67.7782 71.6191
    ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] High confidence RRM2 1.12694 62.9007 70.8854
    256 Measured fructose-1,6-bisphosphatase (ec 3.1.3.11) (d-fructose-1,6-bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:p09467] Low confidence FBP1 1.06171 8216.87 8723.91
    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] High confidence GRAP2 1.22476 6417.19 7859.51
    Ranked max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] MXI1 1.11569 227.999 204.357
    oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Low confidence STT3A 1.04648 199.376 190.521
    Squared formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] High confidence no value 1.303 15465.1 20151
    probable atp-dependent rna helicase ddx10 (dead-box protein 10). [swissprot;acc:q13206] Low confidence DDX10 1.09119 50792.6 46547.8
    Rooted ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] High confidence CEBPZ 1.12665 48.0045 54.0843
    single-minded homolog 1. [swissprot;acc:p81133] Low confidence SIM1 1.05667 67.7782 71.6191
    257 Measured ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] High confidence CUTL1 1.22452 6417.31 7858.12
    synaptojanin 1 (ec 3.1.3.36) (synaptic inositol-1,4,5-trisphosphate 5- phosphatase 1). [swissprot;acc:o43426] Low confidence SYNJ1 1.06157 8082.34 8579.93
    Ranked 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] High confidence DDOST 1.11569 200.691 179.88
    tropomyosin alpha 3 chain (tropomyosin 3) (tropomyosin gamma). [swissprot;acc:p06753] Low confidence TPM3 1.04632 201.316 192.404
    Squared glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840] GYS2 1.09077 53244.4 48813.4
    huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] High confidence no value 1.30229 15482.3 20162.4
    Rooted cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] COMP 1.12591 51.6125 45.8409
    cln3 protein (battenin) (batten disease protein). [swissprot;acc:q13286] Low confidence no value 1.05665 68.3669 72.2396
    258 Measured aflatoxin b1 aldehyde reductase 2 (ec 1.-.-.-) (afb1-ar 2). [swissprot;acc:o95154] AKR7A3 1.06154 9249.74 9818.95
    homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] High confidence CUTL2 1.22449 6417.33 7857.93
    Ranked max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] MXD4 1.11564 227.999 204.366
    tropomyosin 1 alpha chain (alpha-tropomyosin). [swissprot;acc:p09493] Low confidence TPM1 1.04613 201.304 192.427
    Squared adp-ribosylation factor guanine nucleotide factor 6; hepatocellular carcinoma-associated antigen 67. [refseq;acc:nm_015310] PSD3 1.09045 50448.8 46264.1
    huntingtin interacting protein 1 (hip-i). [swissprot;acc:o00291] High confidence HIP1 1.29799 76438 58889.7
    Rooted thrombospondin 3 precursor. [swissprot;acc:p49746] THBS3 1.12589 51.6132 45.8422
    ubiquitin-conjugating enzyme e2 g1 (ec 6.3.2.19) (ubiquitin-protein ligase g1) (ubiquitin carrier protein g1) (e217k) (ubc7). [swissprot;acc:q99462] Low confidence UBE2G1 1.05664 70.3765 74.3627
    259 Measured neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] High confidence WASL 1.22355 6417.81 7852.52
    oligophrenin 1. [swissprot;acc:o60890] Low confidence OPHN1 1.06152 6428.7 6824.22
    Ranked max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] High confidence RAB24 1.11562 227.999 204.37
    trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317] Low confidence PDSS1 1.04599 211.794 202.482
    Squared 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] High confidence COL4A3BP 1.29773 76360.8 58841.7
    trs85 homolog. [swissprot;acc:q9y2l5] Low confidence KIAA1012 1.09045 50448.8 46264.1
    Rooted parafibromin. [refseq;acc:nm_024529] CDC73 1.05662 67.6012 71.4286
    tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] High confidence TFIP11 1.12516 58.2964 65.5926
    260 Measured aflatoxin b1 aldehyde reductase 1 (ec 1.-.-.-) (afb1-ar 1) (aldoketoreductase 7). [swissprot;acc:o43488] Low confidence AKR7A2 1.06147 9246.23 9814.59
    signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] High confidence SRP9 1.22343 4244.95 5193.42
    Ranked ankyrin repeat domain protein 7 (testis-specific protein tsa806). [swissprot;acc:q92527] Low confidence ANKRD7 1.04589 216.855 207.34
    c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] High confidence HS3ST6 1.11394 219.421 196.978
    Squared huntingtin interacting protein 1 related (hip1-related) (hip 12). [swissprot;acc:o75146] HIP1R 1.29752 76296.4 58801.6
    leukemia-associated protein with a cxxc domain. [sptrembl;acc:q8nfu7] Low confidence CXXC6 1.09045 50448.8 46264.1
    Rooted calcineurin b subunit isoform 1 (protein phosphatase 2b regulatory subunit 1) (protein phosphatase 3 regulatory subunit b alpha isoform 1). [swissprot;acc:p06705] WDR92 1.05655 67.4201 71.2324
    multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904] High confidence SCYE1 1.12417 59.0951 66.4332
    261 Measured adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [swissprot;acc:p10109] Low confidence FDX1 1.06133 8837.18 9379.17

    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/