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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2363 to 2412 of 29840 in total
    Interaction Map  : High confidence
    Rank
    		description
    		Value Type
    		Network Comparison Type
    		Filtered
    		red
    		green
    		network_comparison
    148 ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] Squared Divided 1 103496 146848 1.41888
    ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [swissprot;acc:o60858] Subtracted 70011 49783 20228
    sad1/unc-84 protein-like 1. [swissprot;acc:o94901] Ranked Divided 296.677 247.559 1.19841
    sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] Squared Subtracted 0 978.105 1746.18 768.075
    spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [swissprot;acc:q9nrc6] Ranked Divided 6755.71 7863.63 1.164
    symplekin. [swissprot;acc:q92797] Measured Subtracted 1 15213.4 13418.1 1795.3
    149 adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] Squared 0 2783.53 3517.26 733.73
    anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] Divided 1 103496 146848 1.41888
    atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] Ranked 142 170 1.19718
    block 23. [sptrembl;acc:q8nhw5] 0 11469.3 13334.8 1.16265
    cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:p78329] Measured 293.178 379.474 1.29435
    forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] Rooted 1 42.0684 50.4323 1.19882
    interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123] 0 8.52047 10.0173 1.17567
    metaxin 1. [swissprot;acc:q13505] Squared Subtracted 1 60401.6 79875.7 19474.1
    mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [swissprot;acc:p82650] Ranked 0 13942.8 15586.4 1643.6
    neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] Measured Divided 1 11068 8508.5 1.30082
    polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393] Subtracted 0 323.79 544.991 221.201
    potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] Rooted 1 41.6969 28.9696 12.7273
    putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37] Squared Divided 0 8.27669 4.90793 1.68639
    rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] Ranked Subtracted 1 226.582 198.444 28.138
    transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268] Rooted 0 133.419 129.687 3.732
    trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648] Measured 1 11736.6 13531.9 1795.3
    150 amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410] Rooted 42.2825 54.9687 12.6862
    dihydrofolate reductase (ec 1.5.1.3). [swissprot;acc:p00374] Squared 0 3966.2 3268.89 697.31
    dimethylaniline monooxygenase [n-oxide forming] 3 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 3) (fmo 3) (dimethylaniline oxidase 3) (fmo form 2) (fmo ii). [swissprot;acc:p31513] Ranked 7495.26 9130.38 1635.12
    enoyl-coa hydratase, mitochondrial precursor (ec 4.2.1.17) (short chain enoyl-coa hydratase) (sceh) (enoyl-coa hydratase 1). [swissprot;acc:p30084] Squared 1 57913.5 76336.3 18422.8
    estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454] Divided 0 274.947 163.071 1.68606
    metaxin 1. [swissprot;acc:q13505] Measured 933.395 723.368 1.29035
    myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] Ranked 1 55 46 1.19565
    pnas-18. [sptrembl;acc:q9bzu3] Measured Subtracted 0 2256.05 2035.28 220.77
    pre-mrna cleavage complex ii protein clp1. [swissprot;acc:q92989] Squared Divided 1 121200 85473.4 1.41799
    protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] Ranked Subtracted 226.582 198.444 28.138
    protein hspc134 (protein cda04). [swissprot;acc:q9by43] Measured Divided 11068 8508.5 1.30082
    putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361] Rooted 0 26.8649 22.8761 1.17437
    serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323] 1 63.5827 53.0856 1.19774
    small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Measured Subtracted 4172.91 5954.48 1781.57
    zinc finger protein-like 1; zinc-finger protein in men1 region. [refseq;acc:nm_006782] Ranked Divided 0 8730 7516 1.16152
    Rooted Subtracted 19.6214 23.3024 3.681
    151 chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] Divided 1 38.8223 46.4975 1.1977
    cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] Squared 0 25050 42114.6 1.68122
    deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] 1 250303 354894 1.41786
    epoxide hydrolase 1 (ec 3.3.2.3) (microsomal epoxide hydrolase) (epoxide hydratase). [swissprot;acc:p07099] Subtracted 87971.9 69563.1 18408.8
    homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] Rooted 50.3065 62.9788 12.6723
    inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [swissprot;acc:p12268] 0 22.775 19.1245 3.6505
    myosin vc (myosin 5c). [swissprot;acc:q9nqx4] Ranked Divided 1 55 46 1.19565
    orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [swissprot;acc:q9y466] Subtracted 0 7234.6 8858.94 1624.34
    peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570] Squared 396.995 1088.19 691.195
    pre-mrna cleavage complex ii protein clp1. [swissprot;acc:q92989] Measured 1 14830.5 13050.3 1780.2
    protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] Ranked 226.582 198.444 28.138
    sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489] Measured Divided 4578.09 5939.91 1.29746

    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
    - 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/