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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 401 to 450 of 16578 in total
    Value Type  : Ranked
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Network Comparison Type
    		Interaction Map
    		red
    		green
    		network_comparison
    101 F13A1 coagulation factor xiii a chain precursor (ec 2.3.2.13) (protein- glutamine gamma-glutamyltransferase a chain) (transglutaminase a chain). [swissprot;acc:p00488] Subtracted Low confidence 226.395 211.713 14.682
    FOSB protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] High confidence 204.641 161.051 43.59
    MAGEB4 melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] Divided 88.2482 110.265 1.24949
    ROGDI leucine zipper domain protein. [refseq;acc:nm_024589] Low confidence 221.996 238.82 1.07579
    102 DGKQ diacylglycerol kinase, theta (ec 2.7.1.107) (diglyceride kinase) (dgk- theta) (dag kinase theta). [swissprot;acc:p52824] 229.556 213.456 1.07543
    FOSL1 fos-related antigen 1 (fra-1). [swissprot;acc:p15407] Subtracted High confidence 204.642 161.068 43.574
    MAGED2 melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1] Divided 88.2482 110.265 1.24949
    TGM1 protein-glutamine gamma-glutamyltransferase k (ec 2.3.2.13) (transglutaminase k) (tgase k) (tgk) (tg(k)) (transglutaminase 1) (epidermal tgase). [swissprot;acc:p22735] Subtracted Low confidence 226.395 211.713 14.682
    103 COL4A3BP 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] 220.969 235.572 14.603
    JUNB transcription factor jun-b. [swissprot;acc:p17275] High confidence 201.144 158.868 42.276
    PTPRA vacuolar protein sorting 16 (hvps16). [swissprot;acc:q9h269] Divided Low confidence 203.948 189.652 1.07538
    TRO trophinin. [swissprot;acc:q12816] High confidence 88.2482 110.265 1.24949
    104 ADIPOR2 adiponectin receptor 2. [refseq;acc:nm_024551] Low confidence 219.277 204.212 1.07377
    HOMER2 homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] High confidence 252.371 202.016 1.24926
    SLC11A1 natural resistance-associated macrophage protein 1 (nramp 1). [swissprot;acc:p49279] Subtracted Low confidence 225.666 211.107 14.559
    TARDBP tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] High confidence 256.228 298.438 42.21
    105 B9D1 b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] Low confidence 213.243 227.616 14.373
    E2F1 transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [swissprot;acc:q01094] Divided 220.497 205.364 1.07369
    GNB1 guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901] High confidence 266.716 333.165 1.24914
    JUND transcription factor jun-d. [swissprot;acc:p17535] Subtracted 200.941 158.941 42
    106 COQ7 ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] Divided 252.329 202.004 1.24913
    DLGAP3 disks large-associated protein 3 (dap-3) (sap90/psd-95-associated protein 3) (sapap3) (psd-95/sap90 binding protein 3) (fragment). [swissprot;acc:o95886] Subtracted Low confidence 197.731 212.069 14.338
    E2F2 transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] Divided 220.497 205.364 1.07369
    NOSTRIN nostrin. [refseq;acc:nm_052946] Subtracted High confidence 209.299 249.187 39.888
    107 FAM89B mouse mammary turmor virus receptor homolog 1. [refseq;acc:nm_152832] Divided Low confidence 227.429 211.97 1.07293
    HOMER1 homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] High confidence 252.309 201.998 1.24907
    PTPRA vacuolar protein sorting 16 (hvps16). [swissprot;acc:q9h269] Subtracted Low confidence 203.948 189.652 14.296
    SNF8 eap30 subunit of ell complex. [refseq;acc:nm_007241] High confidence 209.299 249.187 39.888
    108 no value disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6] Low confidence 197.752 212.031 14.279
    DLGAP3 disks large-associated protein 3 (dap-3) (sap90/psd-95-associated protein 3) (sapap3) (psd-95/sap90 binding protein 3) (fragment). [swissprot;acc:o95886] Divided 197.731 212.069 1.07251
    HOMER3 homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] High confidence 252.296 201.995 1.24902
    SLC39A6 liv-1 protein, estrogen regulated. [refseq;acc:nm_012319] Subtracted 209.299 249.187 39.888
    109 CREG1 cellular repressor of e1a-stimulated genes. [refseq;acc:nm_003851] Low confidence 197.762 212.013 14.251
    GAD2 glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329] High confidence 209.299 249.187 39.888
    GNB4 guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0] Divided 266.933 333.281 1.24856
    NEURL neuralized-like. [refseq;acc:nm_004210] Low confidence 232.704 216.996 1.07239
    110 no value disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6] 197.752 212.031 1.07221
    CREG2 cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836] Subtracted 197.763 212.011 14.248
    DTX2 deltex 2. [refseq;acc:nm_020892] Divided High confidence 333.144 267.393 1.2459
    NAPG gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747] Subtracted 209.299 249.187 39.888
    111 DLGAP1 disks large-associated protein 1 (dap-1) (guanylate kinase-associated protein) (hgkap) (sap90/psd-95-associated protein 1) (sapap1) (psd- 95/sap90 binding protein 1). [swissprot;acc:o14490] Low confidence 197.779 211.983 14.204
    DTX1 deltex homolog 1; hdx-1. [refseq;acc:nm_004416] Divided High confidence 332.925 267.274 1.24563
    GAD1 glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259] Subtracted 209.299 249.187 39.888
    VPS33A vacuolar protein sorting 33a (hvps33a). [swissprot;acc:q96ax1] Divided Low confidence 203.914 190.189 1.07217
    112 CREG1 cellular repressor of e1a-stimulated genes. [refseq;acc:nm_003851] 197.762 212.013 1.07206
    DLGAP4 disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [swissprot;acc:q9y2h0] Subtracted 197.779 211.983 14.204
    PBK t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492] Divided High confidence 332.874 267.246 1.24557
    POLE4 dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] Subtracted 275.754 235.908 39.846
    113 CREG2 cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836] Divided Low confidence 197.763 212.011 1.07205
    KHDRBS3 kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] High confidence 332.874 267.246 1.24557

    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/