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 51 to 100 of 1345 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Filtered  : 0
    Rank
    		Hugo
    		description
    		Interaction Map
    		red
    		green
    		network_comparison
    26 DTNBP1 dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122] High confidence 12128.3 7533.33 1.60995
    FPGS folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932] Low confidence 9282.29 6526.57 1.42223
    27 no value camp-regulated phosphoprotein 19 (arpp-19) [contains: camp-regulated phosphoprotein 16 (arpp-16)]. [swissprot;acc:p56211] 13109 18516 1.41246
    ptd016 protein. [refseq;acc:nm_016125] High confidence 18050 11234 1.60673
    28 elongation of very long chain fatty acids protein 2. [swissprot;acc:q9nxb9] Low confidence 16116.4 11505 1.40082
    ING5 p28 ing5. [refseq;acc:nm_032329] High confidence 12124.8 7562.05 1.60337
    29 PNMT phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086] 7395 11625 1.57201
    SLC12A9 solute carrier family 12 (potassium/chloride transporters), member 9; cation-chloride cotransporter-interacting protein. [refseq;acc:nm_020246] Low confidence 12129.6 8687.07 1.39628
    30 no value alpha 2 globin. [refseq;acc:nm_000517] 11486.2 15987.1 1.39185
    beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938] High confidence 7395 11625 1.57201
    31 hemoglobin gamma-a and gamma-g chains. [swissprot;acc:p02096] Low confidence 11485.6 15984.3 1.39168
    LRRFIP1 leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735] High confidence 8082.33 5266.67 1.53462
    32 no value importin 9. [refseq;acc:nm_018085] 13292.2 8691.76 1.52929
    myoglobin. [swissprot;acc:p02144] Low confidence 11485.4 15983.3 1.39162
    33 nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [swissprot;acc:q99733] High confidence 13292.2 8691.76 1.52929
    FKBP6 fk506-binding protein 6 (ec 5.2.1.8) (peptidyl-prolyl cis-trans isomerase) (ppiase) (rotamase) (36 kda fk506 binding protein) (fkbp- 36) (immunophilin fkbp36). [swissprot;acc:o75344] Low confidence 20324.1 14746.1 1.37827
    34 FBN3 fibrillin 3. [refseq;acc:nm_032447] 5450.5 7506.66 1.37724
    MAPRE2 microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268] High confidence 11284 17173.8 1.52196
    35 no value nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] 3208.8 4871.6 1.5182
    PTP4A2 protein tyrosine phosphatase type iva, member 2 isoform 1; protein tyrosine phosphatase iva2; protein tyrosine phosphatase iva; phosphatase of regenerating liver 2. [refseq;acc:nm_003479] Low confidence 11808.5 16243 1.37553
    36 GNB1L guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [swissprot;acc:q9byb4] High confidence 22422 14964 1.4984
    SAMSN1 sam-domain protein samsn-1 (sam domain, sh3 domain and nuclear localisation signals protein 1). [swissprot;acc:q9nsi8] Low confidence 13052.7 9520.8 1.37097
    37 no value dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0] High confidence 3859 2582 1.49458
    MTMR8 myotubularin related protein 8. [refseq;acc:nm_017677] Low confidence 12302 8993.6 1.36786
    38 CDK8 cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336] High confidence 7230 10771 1.48976
    MLXIPL williams-beuren syndrome chromosome region 14 protein (ws basic-helix- loop-helix leucine zipper protein) (ws-bhlh) (mlx interactor). [swissprot;acc:q9np71] Low confidence 6768.72 9243.55 1.36563
    39 no value ero1-like. [refseq;acc:nm_014584] High confidence 13853 20536 1.48242
    BET1L blocked early in transport 1 homolog (s. cerevisiae) like; golgi snare 15 kda protein. [refseq;acc:nm_016526] Low confidence 11290 8270.5 1.36509
    40 no value filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] High confidence 3845 5699 1.48218
    GNPDA1 glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926] Low confidence 11761 15924 1.35397
    41 no value 60s ribosomal protein l21. [swissprot;acc:p46778] High confidence 9994.33 6758.83 1.47871
    nadh-ubiquinone oxidoreductase mlrq subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-mlrq) (ci-mlrq). [swissprot;acc:o00483] Low confidence 8655 6435 1.34499
    42 mesoderm induction early response 1. [refseq;acc:nm_020948] 6489.72 8709.15 1.34199
    SLC25A6 adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236] High confidence 8158 5530.5 1.47509
    43 no value pnas-129. [sptrembl;acc:q9bxv8] Low confidence 11107.6 14842.4 1.33624
    GSTT2B glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712] High confidence 12143.8 8356.02 1.4533
    44 ING5 p28 ing5. [refseq;acc:nm_032329] Low confidence 12418.8 9391.47 1.32235
    SERPINB12 serpin b12. [swissprot;acc:q96p63] High confidence 14604.2 21138.6 1.44743
    45 no value hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8] 14592 21113.7 1.44694
    zona pellucida sperm-binding protein 3 precursor (zona pellucida glycoprotein zp3) (zona pellucida protein c) (sperm receptor) (zp3a/zp3b). [swissprot;acc:p21754] Low confidence 10665.2 14025.1 1.31503
    46 60s ribosomal protein l37a. [swissprot;acc:p12751] High confidence 12941.7 18499.2 1.42943
    synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] Low confidence 17361.7 13210.4 1.31424
    47 CYP27B1 25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [swissprot;acc:o15528] High confidence 12941.7 18499.2 1.42943
    NUP43 nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] Low confidence 4338.65 5700.79 1.31395
    48 NDUFA5 nadh-ubiquinone oxidoreductase 13 kda-b subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-b) (ci-13kd-b) (complex i subunit b13). [swissprot;acc:q16718] High confidence 9830 6909 1.42278
    POM121L2 b24o18.3 (pom121 membrane glycoprotein (rat homolog)-like 2). [sptrembl;acc:q96kw2] Low confidence 10664.4 14002.9 1.31305
    49 no value brain protein 16. [refseq;acc:nm_016458] High confidence 6890.54 4854.99 1.41927
    TRAPPC1 bet5 homolog (multiple myeloma protein 2) (mum-2). [swissprot;acc:q9y5r8] Low confidence 14607.1 11141.9 1.31101
    50 COMP cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] High confidence 9249.73 13091.4 1.41533
    FBP2 fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] Low confidence 9449.27 12378.5 1.31

    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/