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 Filtered Interaction Map red green network_comparison
    Results: HTML CSV LaTeX Showing element 51 to 100 of 3730 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Rank
    		Hugo
    		description
    		Filtered
    		red
    		green
    		network_comparison
    26 DTNBP1 dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122] 0 12128.3 7533.33 1.60995
    PANK3 pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] 1 58 44 1.31818
    27 no value ptd016 protein. [refseq;acc:nm_016125] 0 18050 11234 1.60673
    SLC25A43 mitochondrial solute carrier protein. [refseq;acc:nm_145305] 1 58 44 1.31818
    28 ATF3 cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] 201.949 153.671 1.31416
    ING5 p28 ing5. [refseq;acc:nm_032329] 0 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
    PPP2R2D uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] 1 187.458 243.678 1.29991
    30 no value beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938] 0 7395 11625 1.57201
    serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [swissprot;acc:q00007] 1 187.457 243.678 1.29991
    31 LRRFIP1 leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735] 0 8082.33 5266.67 1.53462
    PPP2R2B serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [swissprot;acc:q00005] 1 187.458 243.677 1.2999
    32 no value importin 9. [refseq;acc:nm_018085] 0 13292.2 8691.76 1.52929
    PPP2R2C serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [swissprot;acc:q9y2t4] 1 187.462 243.673 1.29985
    33 no value nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [swissprot;acc:q99733] 0 13292.2 8691.76 1.52929
    PPP2R1B serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, beta isoform (pp2a, subunit a, pr65-beta isoform) (pp2a, subunit a, r1-beta isoform). [swissprot;acc:p30154] 1 188.688 242.742 1.28647
    34 MAPRE2 microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268] 0 11284 17173.8 1.52196
    PPP2R1A serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [swissprot;acc:p30153] 1 189.07 242.453 1.28235
    35 no value nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] 0 3208.8 4871.6 1.5182
    NFYC nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952] 1 260.532 204.309 1.27519
    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] 0 22422 14964 1.4984
    NFYA ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511] 1 260.532 204.309 1.27519
    37 no value dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0] 0 3859 2582 1.49458
    PPP1R14A protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] 1 322 253 1.27273
    38 CDK8 cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336] 0 7230 10771 1.48976
    MFAP4 microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] 1 322 253 1.27273
    39 no value ero1-like. [refseq;acc:nm_014584] 0 13853 20536 1.48242
    PPP1R14D protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] 1 322 253 1.27273
    40 no value filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] 0 3845 5699 1.48218
    FCN2 ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485] 1 322 253 1.27273
    41 no value 60s ribosomal protein l21. [swissprot;acc:p46778] 0 9994.33 6758.83 1.47871
    protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] 1 322 253 1.27273
    42 FOS proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] 204.641 160.957 1.2714
    SLC25A6 adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236] 0 8158 5530.5 1.47509
    43 no value jun dimerization protein. [refseq;acc:nm_130469] 1 204.641 160.957 1.2714
    GSTT2B glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712] 0 12143.8 8356.02 1.4533
    44 FOSL2 fos-related antigen 2. [swissprot;acc:p15408] 1 204.641 161.046 1.2707
    SERPINB12 serpin b12. [swissprot;acc:q96p63] 0 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
    FOSB protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] 1 204.641 161.051 1.27066
    46 no value 60s ribosomal protein l37a. [swissprot;acc:p12751] 0 12941.7 18499.2 1.42943
    FOSL1 fos-related antigen 1 (fra-1). [swissprot;acc:p15407] 1 204.642 161.068 1.27053
    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] 0 12941.7 18499.2 1.42943
    TMEM132A gbp protein isoform a. [refseq;acc:nm_017870] 1 325.586 256.492 1.26938
    48 GABARAP gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] 65.4586 83.0461 1.26868
    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] 0 9830 6909 1.42278
    49 no value brain protein 16. [refseq;acc:nm_016458] 6890.54 4854.99 1.41927
    ARRB2 beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] 1 133 105 1.26667
    50 ARRB1 beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]
    COMP cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] 0 9249.73 13091.4 1.41533

    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/