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 network_comparison green
    Results: HTML CSV LaTeX Showing element 3001 to 3050 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		Network Comparison Type
    		red
    		network_comparison
    		green
    376 no value 40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] Rooted Divided 50.2554 1.10285 45.5688
    ADCY5 adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] Ranked Subtracted 248.152 19.074 267.226
    C10orf83 44050 protein. [refseq;acc:nm_178832] Measured Divided 17385.9 1.16769 14889.2
    DDX56 probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] Ranked 257.017 1.09395 234.945
    GRB2 growth factor receptor-bound protein 2 (grb2 adapter protein) (sh2/sh3 adapter grb2) (ash protein). [swissprot;acc:p29354] Rooted Subtracted 61.2684 6.4866 67.755
    HOMER1 homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] Measured 4251.65 960.68 5212.33
    LGALS4 galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470] Squared Divided 46021.4 1.2345 56813.2
    UGP2 utp--glucose-1-phosphate uridylyltransferase 2 (ec 2.7.7.9) (udp- glucose pyrophosphorylase 2) (udpgp 2) (ugpase 2). [swissprot;acc:q16851] Subtracted 29544.1 6134.2 35678.3
    377 HOMER3 homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] Measured 4252.66 960.39 5213.05
    LRRC15 leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] Ranked 248.152 19.074 267.226
    MRPL2 mitochondrial ribosomal protein l2. [refseq;acc:nm_015950] Rooted Divided 50.2554 1.10285 45.5687
    NEK2 serine/threonine-protein kinase nek2 (ec 2.7.1.37) (nima-related protein kinase 2) (nima-like protein kinase 1) (hspk 21). [swissprot;acc:p51955] Subtracted 61.2684 6.4866 67.755
    ODC1 ornithine decarboxylase (ec 4.1.1.17) (odc). [swissprot;acc:p11926] Squared Divided 33044.9 1.23412 40781.4
    POLR1A dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [swissprot;acc:o95602] Ranked 242.691 1.09391 265.481
    PPP1R8 nuclear inhibitor of protein phosphatase-1 (nipp-1) (protein phosphatase 1, regulatory inhibitor subunit 8) [includes: activator of rna decay (ec 3.1.4.-) (ard-1)]. [swissprot;acc:q12972] Measured 17385.9 1.16769 14889.2
    UBE2V2 ubiquitin-conjugating enzyme e2 variant 2; 1 alpha,25-dihydroxyvitamin d3-inducible; enterocyte differentiation promoting factor; methyl methanesulfonate sensitive 2, s. cerevisiae, homolog of. [refseq;acc:nm_003350] Squared Subtracted 29540.4 6132.2 35672.6
    378 DDX56 probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] Rooted 47.3621 6.4734 53.8355
    EIF4G3 eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] Squared Divided 15034.5 1.23398 18552.2
    FEM1B fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322] Ranked Subtracted 248.152 19.074 267.226
    MRPL4 mitochondrial ribosomal protein l4 isoform a. [refseq;acc:nm_015956] Rooted Divided 50.5816 1.10263 45.8738
    NFU1 hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] Measured 12471.7 1.16758 14561.7
    PARD6G partitioning defective-6 homolog gamma (par-6 gamma) (par6d). [swissprot;acc:q9byg4] Squared Subtracted 30286.5 6075.5 36362
    RPL30 60s ribosomal protein l30. [swissprot;acc:p04645] Ranked Divided 242.593 1.09387 265.365
    SORBS3 vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504] Measured Subtracted 6272.91 953.15 7226.06
    379 AASS aminoadipate-semialdehyde synthase; lysine-ketoglutarate reductase /saccharopine dehydrogenase; lysine-2-oxoglutarate reductase; aminoadipic semialdehyde synthase. [refseq;acc:nm_005763] Squared Divided 33010.8 1.23391 40732.2
    AK2 adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p54819] Ranked 241.509 1.0938 264.163
    CLEC11A stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [refseq;acc:nm_002975] Rooted Subtracted 86.5959 6.4725 93.0684
    GULP1 ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315] Divided 59.5128 1.10235 65.604
    LRRC3 leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71] Ranked Subtracted 248.152 19.074 267.226
    RRM2 ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] Measured Divided 6704.44 1.16512 7811.45
    SRP9 signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Subtracted 4244.95 948.47 5193.42
    TUB tubby protein homolog. [swissprot;acc:p50607] Squared 30286.5 6075.5 36362
    380 no value suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169] Ranked Divided 242.109 1.09368 264.79
    ACADVL acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] Measured 12998.5 1.16461 15138.2
    ADC ornithine decarboxylase-like protein (ec 4.1.1.17) (odc-paralogue) (odc-p). [swissprot;acc:q96a70] Squared 32991.5 1.23379 40704.5
    CAPS calcyphosine. [swissprot;acc:q13938] Rooted 59.5128 1.10235 65.604
    LAMC1 laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047] Ranked Subtracted 248.152 19.074 267.226
    NUBP1 nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] Measured 4641.09 947.66 5588.75
    PRKCI protein kinase c, iota type (ec 2.7.1.37) (npkc-iota) (atypical protein kinase c-lamda/iota) (apkc-lambda/iota). [swissprot;acc:p41743] Squared 30286.5 6075.5 36362
    TRMU trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648] Rooted 96.6463 6.4567 103.103
    381 AZIN1 ornithine decarboxylase antizyme inhibitor. [swissprot;acc:o14977] Squared Divided 32987.4 1.23376 40698.5
    CLEC3A c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596] Rooted Subtracted 86.4264 6.4371 92.8635
    CRNKL1 crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] Divided 59.5128 1.10235 65.604
    NUBP2 nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] Measured Subtracted 4641.09 947.66 5588.75
    NUMB numb protein homolog (h-numb) (protein s171). [swissprot;acc:p49757] Squared 30286.5 6075.5 36362
    SCYE1 multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904] Measured Divided 5246.01 1.16456 6109.31
    SLC46A2 thymic stromal co-transporter. [refseq;acc:nm_033051] Ranked Subtracted 248.152 19.074 267.226
    TAF7 transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545] Divided 200.586 1.09357 183.423
    382 no value rna-binding protein. [refseq;acc:nm_019027] Squared 15043.7 1.23375 18560.1
    DDX54 atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072] Ranked Subtracted 253.852 19.044 234.808

    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/