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 Hugo Interaction Map network_comparison Filtered red green
    Results: HTML CSV LaTeX Showing element 56024 to 56073 of 66312 in total
    Network Comparison Type  : Subtracted
    Filtered  : 1
    Rank
    		Value Type
    		description
    		Hugo
    		Interaction Map
    		network_comparison
    		red
    		green
    2859 Ranked ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260] no value Low confidence 3.397 202.757 199.36
    Squared homeobox protein nkx-6.1. [swissprot;acc:p78426] NKX6-1 High confidence 0 0 0
    nuclear factor nf-kappa-b p105 subunit (dna-binding factor kbf1) (ebp- 1) [contains: nuclear factor nf-kappa-b p50 subunit]. [swissprot;acc:p19838] NFKB1 Low confidence 1569.4 45008.1 43438.7
    Rooted 60s ribosomal protein l39. [swissprot;acc:p02404] no value 2.3441 71.5491 73.8932
    homeobox protein nkx-6.1. [swissprot;acc:p78426] NKX6-1 High confidence 0 0 0
    2860 Measured dual specificity mitogen-activated protein kinase kinase 6 (ec 2.7.1.-) (map kinase kinase 6) (mapkk 6) (mapk/erk kinase 6) (sapkk3). [swissprot;acc:p52564] MAP2K6 Low confidence 228.48 7942.93 8171.41
    importin 9. [refseq;acc:nm_018085] no value High confidence 0 0 0
    Ranked
    sprouty-related protein with evh-1 domain 1. [refseq;acc:nm_152594] SPRED1 Low confidence 3.397 200.203 196.806
    Squared importin 9. [refseq;acc:nm_018085] no value High confidence 0 0 0
    nf-kappab inhibitor beta (nf-kappa-bib) (i-kappa-b-beta) (ikappabbeta) (ikb-beta) (ikb-b) (thyroid receptor interacting protein 9) (tr- interacting protein 9). [swissprot;acc:q15653] NFKBIB Low confidence 1569.4 45008 43438.6
    Rooted importin 9. [refseq;acc:nm_018085] no value High confidence 0 0 0
    solute carrier family 23, member 1 (sodium-dependent vitamin c transporter 1) (hsvct1) (na(+)/l-ascorbic acid transporter 1) (yolk sac permease-like molecule 3). [swissprot;acc:q9uhi7] SLC23A1 Low confidence 2.344 71.767 74.111
    2861 Measured glucosamine-6-phosphate isomerase. [refseq;acc:nm_138335] GNPDA2 High confidence 0 0 0
    spermatogenesis associated 6. [refseq;acc:nm_019073] SPATA6 Low confidence 228.46 7945.87 8174.33
    Ranked glucosamine-6-phosphate isomerase. [refseq;acc:nm_138335] GNPDA2 High confidence 0 0 0
    serine/threonine-protein kinase h1 (ec 2.7.1.37) (psk-h1). [swissprot;acc:p11801] PSKH1 Low confidence 3.397 197.044 193.647
    Squared glucosamine-6-phosphate isomerase. [refseq;acc:nm_138335] GNPDA2 High confidence 0 0 0
    nuclear factor nf-kappa-b p100/p49 subunits (h2tf1) (oncogene lyt-10) (lyt10) [contains: nuclear factor nf-kappa-b p52 subunit]. [swissprot;acc:q00653] NFKB2 Low confidence 1569.4 45008 43438.6
    Rooted eukaryotic translation initiation factor 5a (eif-5a) (eif-4d) (rev- binding factor). [swissprot;acc:p10159] EIF5AP1 2.344 73.0871 75.4311
    glucosamine-6-phosphate isomerase. [refseq;acc:nm_138335] GNPDA2 High confidence 0 0 0
    2862 Measured c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] HS3ST6 Low confidence 228.37 7807.4 8035.77
    syndecan-3 (synd3). [swissprot;acc:o75056] SDC3 High confidence 0 0 0
    Ranked nuclear autoantigenic sperm protein (nasp). [swissprot;acc:p49321] NASP Low confidence 3.397 201.282 197.885
    syndecan-3 (synd3). [swissprot;acc:o75056] SDC3 High confidence 0 0 0
    Squared epidermal growth factor receptor pathway substrate 8-like protein 2; eps8-related protein 2; epidermal growth factor receptor pathway substrate 8-related protein 2. [refseq;acc:nm_022772] EPS8L2 Low confidence 1569.3 43620 42050.7
    syndecan-3 (synd3). [swissprot;acc:o75056] SDC3 High confidence 0 0 0
    Rooted solute carrier family 23, member 2 (sodium-dependent vitamin c transporter 2) (hsvct2) (na(+)/l-ascorbic acid transporter 2) (yolk sac permease-like molecule 2) (nucleobase transporter-like 1 protein). [swissprot;acc:q9ugh3] SLC23A2 Low confidence 2.344 71.767 74.111
    syndecan-3 (synd3). [swissprot;acc:o75056] SDC3 High confidence 0 0 0
    2863 Measured heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042] HS3ST3A1 Low confidence 228.37 7807.4 8035.77
    high-glucose-regulated protein 8 (ny-ren-2 antigen). [swissprot;acc:q9y5a9] no value High confidence 0 0 0
    Ranked
    stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [refseq;acc:nm_002975] CLEC11A Low confidence 3.396 194.013 190.617
    Squared f-box and leucine-rich repeat protein 7; f-box protein fbl7. [refseq;acc:nm_012304] FBXL7 1569 45613.6 44044.6
    high-glucose-regulated protein 8 (ny-ren-2 antigen). [swissprot;acc:q9y5a9] no value High confidence 0 0 0
    Rooted
    steroid hormone receptor err2 (estrogen-related receptor, beta) (err-beta) (estrogen receptor-like 2) (err beta-2). [swissprot;acc:o95718] ESRRB Low confidence 2.3434 72.9407 75.2841
    2864 Measured heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041] HS3ST3B1 228.37 7807.4 8035.77
    mago nashi protein homolog. [swissprot;acc:p50606] MAGOH High confidence 0 0 0
    Ranked bone morphogenetic protein 7 precursor (bmp-7) (osteogenic protein 1) (op-1). [swissprot;acc:p18075] BMP7 Low confidence 3.396 203.455 200.059
    mago nashi protein homolog. [swissprot;acc:p50606] MAGOH High confidence 0 0 0
    Squared
    tubulin beta-2 chain. [swissprot;acc:p05217] TUBB2B Low confidence 1568.8 41902.1 40333.3
    Rooted hydroxyacid oxidase 2 (ec 1.1.3.15) (haox2) ((s)-2-hydroxy-acid oxidase, peroxisomal) (long chain alpha-hydroxy acid oxidase) (long- chain l-2-hydroxy acid oxidase). [swissprot;acc:q9nyq3] HAO2 2.3429 70.5139 72.8568
    mago nashi protein homolog. [swissprot;acc:p50606] MAGOH High confidence 0 0 0
    2865 Measured heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043] HS3ST2 Low confidence 228.37 7807.4 8035.77
    t-cell acute lymphocytic leukemia-1 protein (tal-1 protein) (stem cell protein) (t-cell leukemia/lymphoma-5 protein). [swissprot;acc:p17542] TAL1 High confidence 0 0 0
    Ranked ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260] no value Low confidence 3.395 202.759 199.364
    t-cell acute lymphocytic leukemia-1 protein (tal-1 protein) (stem cell protein) (t-cell leukemia/lymphoma-5 protein). [swissprot;acc:p17542] TAL1 High confidence 0 0 0
    Squared sphingolipid delta 4 desaturase; membrane fatty acid (lipid) desaturase; dihydroceramide desaturase. [refseq;acc:nm_003676] DEGS1 Low confidence 1568.2 45277.2 43709

    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/