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 1 to 50 of 502 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 0
    Rank
    		Hugo
    		description
    		red
    		green
    		network_comparison
    1 ARFGAP3 adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] 4294 15915 3.70633
    2 STARD3 mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] 5865 14977 2.55362
    3 no value nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] 4475.84 11083.9 2.47638
    4 mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 8906 21883 2.45711
    5 ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855] 5510.5 11965.7 2.17144
    6 UBE3B ubiquitin protein ligase. [refseq;acc:nm_130466] 7523 15339.2 2.03897
    7 PERLD1 cab2. [refseq;acc:nm_033419] 21866 10950 1.99689
    8 no value nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] 11525 21888 1.89918
    9 TBL1Y transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]
    10 FBP2 fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] 7509.39 14178.1 1.88805
    11 ATP9A potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110] 11627 6248 1.86092
    12 FPGS folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932] 9429.18 5208.84 1.81023
    13 no value heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107] 5210.5 9264.5 1.77804
    14 dystrophin. [swissprot;acc:p11532] 10232.5 18054.8 1.76446
    15 succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [swissprot;acc:o14521] 19403 11267 1.72211
    16 CCNH cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946] 12170.7 20670.6 1.69839
    17 no value fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402] 11543 6812 1.69451
    18 homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 22286 13216 1.68629
    19 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]
    20 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]
    21 ACRC acrc protein; putative nuclear protein. [refseq;acc:nm_052957] 6313.38 10621.4 1.68236
    22 PNPO pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] 20989 12479 1.68195
    23 HGS hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712] 15520.4 9285.44 1.67148
    24 no value ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] 13730.5 8257 1.66289
    25 lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]
    26 DTNBP1 dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122] 12128.3 7533.33 1.60995
    27 no value ptd016 protein. [refseq;acc:nm_016125] 18050 11234 1.60673
    28 ING5 p28 ing5. [refseq;acc:nm_032329] 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
    30 no value beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]
    31 LRRFIP1 leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735] 8082.33 5266.67 1.53462
    32 no value importin 9. [refseq;acc:nm_018085] 13292.2 8691.76 1.52929
    33 nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [swissprot;acc:q99733]
    34 MAPRE2 microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268] 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
    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] 22422 14964 1.4984
    37 no value dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0] 3859 2582 1.49458
    38 CDK8 cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336] 7230 10771 1.48976
    39 no value ero1-like. [refseq;acc:nm_014584] 13853 20536 1.48242
    40 filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] 3845 5699 1.48218
    41 60s ribosomal protein l21. [swissprot;acc:p46778] 9994.33 6758.83 1.47871
    42 SLC25A6 adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236] 8158 5530.5 1.47509
    43 GSTT2B glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712] 12143.8 8356.02 1.4533
    44 SERPINB12 serpin b12. [swissprot;acc:q96p63] 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
    46 60s ribosomal protein l37a. [swissprot;acc:p12751] 12941.7 18499.2 1.42943
    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]
    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] 9830 6909 1.42278
    49 no value brain protein 16. [refseq;acc:nm_016458] 6890.54 4854.99 1.41927
    50 COMP cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] 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/