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 Hugo Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 3051 to 3100 of 6456 in total
    Value Type  : Ranked
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Network Comparison Type
    		red
    		green
    		network_comparison
    1526 cadherin-related tumor suppressor homolog precursor (fat protein homolog). [swissprot;acc:q14517] FAT Divided 219.306 223.179 1.01766
    dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [swissprot;acc:p42658] DPP6 Subtracted 213.267 209.511 3.756
    1527 mln64 n-terminal domain homolog (stard3 n-terminal like protein). [swissprot;acc:o95772] STARD3NL Divided 219.306 223.179 1.01766
    seprase (ec 3.4.21.-) (fibroblast activation protein alpha) (integral membrane serine protease) (170-kda melanoma membrane-bound gelatinase). [swissprot;acc:q12884] FAP Subtracted 213.267 209.511 3.756
    1528 af-6 protein. [swissprot;acc:p55196] MLLT4 218.733 214.98 3.753
    hepatocyte nuclear factor 3-gamma (hnf-3g) (forkhead box protein a3) (fork head-related protein fkh h3). [swissprot;acc:p55318] FOXA3 Divided 217.785 214.021 1.01759
    1529 actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571] ACTG1 216.762 213.031 1.01751
    myb proto-oncogene protein (c-myb). [swissprot;acc:p10242] MYB Subtracted 222.672 218.92 3.752
    1530 af-6 protein. [swissprot;acc:p55196] MLLT4 Divided 218.733 214.98 1.01746
    m-phase inducer phosphatase 2 (ec 3.1.3.48) (dual specificity phosphatase cdc25b). [swissprot;acc:p30305] CDC25B Subtracted 260.269 256.531 3.738
    1531 cysteine-rich motor neuron 1; cysteine-rich repeat-containing protein s52 precursor. [refseq;acc:nm_016441] CRIM1 Divided 217.025 213.304 1.01744
    dynactin complex 50 kda subunit (50 kda dynein-associated polypeptide) (dynamitin) (dctn-50) (dynactin 2). [swissprot;acc:q13561] DCTN2 Subtracted 225.159 221.424 3.735
    1532 adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236] SLC25A6
    rna-binding protein 10 (rna binding motif protein 10) (dxs8237e). [swissprot;acc:p98175] RBM10 Divided 228.419 232.376 1.01732
    1533 adp,atp carrier protein, heart/skeletal muscle isoform t1 (adp/atp translocase 1) (adenine nucleotide translocator 1) (ant 1). [swissprot;acc:p12235] SLC25A4 Subtracted 225.159 221.424 3.735
    cytochrome c. [swissprot;acc:p00001] CYCS Divided 228.419 232.376 1.01732
    1534 heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174] HS6ST2
    [3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial precursor (ec 2.7.1.115) (branched-chain alpha-ketoacid dehydrogenase kinase) (bckdhkin) (bckd-kinase). [swissprot;acc:o14874] BCKDK Subtracted 213.259 209.524 3.735
    1535 adp,atp carrier protein, fibroblast isoform (adp/atp translocase 2) (adenine nucleotide translocator 2) (ant 2). [swissprot;acc:p05141] SLC25A5 225.159 221.424
    heparan sulfate 6-o-sulfotransferase; heparan-sulfate 6-sulfotransferase. [refseq;acc:nm_004807] HS6ST1 Divided 228.419 232.376 1.01732
    1536 actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571] ACTG1 Subtracted 216.762 213.031 3.731
    fatty acid hydroxylase domain containing 1. [refseq;acc:nm_024306] FA2H Divided 228.419 232.376 1.01732
    1537 cysteine-rich motor neuron 1; cysteine-rich repeat-containing protein s52 precursor. [refseq;acc:nm_016441] CRIM1 Subtracted 217.025 213.304 3.721
    ww domain binding protein 11; npw38-binding protein npwbp; sh3 domain-binding protein snp70. [refseq;acc:nm_016312] WBP11 Divided 228.419 232.376 1.01732
    1538 elac homolog 2; putative prostate cancer susceptibility protein; elac (e. coli) homolog 2. [refseq;acc:nm_018127] ELAC2
    myb-related protein b (b-myb). [swissprot;acc:p10244] MYBL2 Subtracted 222.541 218.823 3.718
    1539 myb-related protein a (a-myb). [swissprot;acc:p10243] MYBL1 222.512 218.802 3.71
    rna-binding protein 5 (rna binding motif protein 5) (putative tumor suppressor luca15) (g15 protein). [swissprot;acc:p52756] RBM5 Divided 228.419 232.376 1.01732
    1540 argininosuccinate synthase (ec 6.3.4.5) (citrulline--aspartate ligase). [swissprot;acc:p00966] ASS1 Subtracted 217.769 221.474 3.705
    autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0] ATG5 Divided 240.077 236.015 1.01721
    1541 importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [swissprot;acc:p55060] CSE1L Subtracted 192.336 188.637 3.699
    myb proto-oncogene protein (c-myb). [swissprot;acc:p10242] MYB Divided 222.672 218.92 1.01714
    1542 orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [swissprot;acc:q9y466] NR2E1 Subtracted 219.762 216.081 3.681
    trimethyllysine dioxygenase, mitochondrial precursor (ec 1.14.11.8) (epsilon-trimethyllysine 2-oxoglutarate dioxygenase) (tml-alpha- ketoglutarate dioxygenase) (tml hydroxylase) (tml dioxygenase) (tmld). [swissprot;acc:q9nvh6] TMLHE Divided 213.546 209.965 1.01706
    1543 gtp-binding protein era homolog (hera) (fragment). [swissprot;acc:o75616] ERAL1
    orphan nuclear receptor tr2. [swissprot;acc:p13056] NR2C1 Subtracted 219.76 216.083 3.677
    1544 orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [swissprot;acc:q9y466] NR2E1 Divided 219.762 216.081 1.01704
    thymidylate synthase (ec 2.1.1.45) (ts) (tsase). [swissprot;acc:p04818] TYMS Subtracted 225.119 228.769 3.65
    1545 dihydrofolate reductase (ec 1.5.1.3). [swissprot;acc:p00374] no value
    orphan nuclear receptor tr2. [swissprot;acc:p13056] NR2C1 Divided 219.76 216.083 1.01702
    1546 argininosuccinate synthase (ec 6.3.4.5) (citrulline--aspartate ligase). [swissprot;acc:p00966] ASS1 217.769 221.474 1.01701
    stromal cell-derived factor 2 precursor (sdf-2). [swissprot;acc:q99470] SDF2 Subtracted 225.119 228.769 3.65
    1547 myb-related protein b (b-myb). [swissprot;acc:p10244] MYBL2 Divided 222.541 218.823 1.01699
    stromal cell-derived factor 2-like protein 1 precursor (sdf2 like protein 1) (pwp1-interacting protein 8). [swissprot;acc:q9hcn8] SDF2L1 Subtracted 225.119 228.769 3.65
    1548 eukaryotic translation initiation factor 3 subunit 11 (eif-3 p25) (eif3k) (muscle specific gene m9 protein) (ptd001) (hspc029) (arg134). [swissprot;acc:q9ubq5] EIF3K 221.128 224.767 3.639
    myb-related protein a (a-myb). [swissprot;acc:p10243] MYBL1 Divided 222.512 218.802 1.01696
    1549 dynactin complex 50 kda subunit (50 kda dynein-associated polypeptide) (dynamitin) (dctn-50) (dynactin 2). [swissprot;acc:q13561] DCTN2 225.159 221.424 1.01687
    erythroid differentiation and denucleation factor 1. [swissprot;acc:o60584] SLMO1 Subtracted 221.128 224.767 3.639
    1550 adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236] SLC25A6 Divided 225.159 221.424 1.01687
    bardet-biedl syndrome 7 protein isoform a; bbs2-like 1. [refseq;acc:nm_176824] BBS7 Subtracted 221.128 224.767 3.639

    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/