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 Network Comparison Type Value Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 3075 to 3124 of 6456 in total
    Value Type  : Ranked
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Network Comparison Type
    		red
    		network_comparison
    		green
    1538 ELAC2 elac homolog 2; putative prostate cancer susceptibility protein; elac (e. coli) homolog 2. [refseq;acc:nm_018127] Divided 228.419 1.01732 232.376
    MYBL2 myb-related protein b (b-myb). [swissprot;acc:p10244] Subtracted 222.541 3.718 218.823
    1539 MYBL1 myb-related protein a (a-myb). [swissprot;acc:p10243] 222.512 3.71 218.802
    RBM5 rna-binding protein 5 (rna binding motif protein 5) (putative tumor suppressor luca15) (g15 protein). [swissprot;acc:p52756] Divided 228.419 1.01732 232.376
    1540 ASS1 argininosuccinate synthase (ec 6.3.4.5) (citrulline--aspartate ligase). [swissprot;acc:p00966] Subtracted 217.769 3.705 221.474
    ATG5 autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0] Divided 240.077 1.01721 236.015
    1541 CSE1L importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [swissprot;acc:p55060] Subtracted 192.336 3.699 188.637
    MYB myb proto-oncogene protein (c-myb). [swissprot;acc:p10242] Divided 222.672 1.01714 218.92
    1542 NR2E1 orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [swissprot;acc:q9y466] Subtracted 219.762 3.681 216.081
    TMLHE 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] Divided 213.546 1.01706 209.965
    1543 ERAL1 gtp-binding protein era homolog (hera) (fragment). [swissprot;acc:o75616]
    NR2C1 orphan nuclear receptor tr2. [swissprot;acc:p13056] Subtracted 219.76 3.677 216.083
    1544 NR2E1 orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [swissprot;acc:q9y466] Divided 219.762 1.01704 216.081
    TYMS thymidylate synthase (ec 2.1.1.45) (ts) (tsase). [swissprot;acc:p04818] Subtracted 225.119 3.65 228.769
    1545 no value dihydrofolate reductase (ec 1.5.1.3). [swissprot;acc:p00374]
    NR2C1 orphan nuclear receptor tr2. [swissprot;acc:p13056] Divided 219.76 1.01702 216.083
    1546 ASS1 argininosuccinate synthase (ec 6.3.4.5) (citrulline--aspartate ligase). [swissprot;acc:p00966] 217.769 1.01701 221.474
    SDF2 stromal cell-derived factor 2 precursor (sdf-2). [swissprot;acc:q99470] Subtracted 225.119 3.65 228.769
    1547 MYBL2 myb-related protein b (b-myb). [swissprot;acc:p10244] Divided 222.541 1.01699 218.823
    SDF2L1 stromal cell-derived factor 2-like protein 1 precursor (sdf2 like protein 1) (pwp1-interacting protein 8). [swissprot;acc:q9hcn8] Subtracted 225.119 3.65 228.769
    1548 EIF3K eukaryotic translation initiation factor 3 subunit 11 (eif-3 p25) (eif3k) (muscle specific gene m9 protein) (ptd001) (hspc029) (arg134). [swissprot;acc:q9ubq5] 221.128 3.639 224.767
    MYBL1 myb-related protein a (a-myb). [swissprot;acc:p10243] Divided 222.512 1.01696 218.802
    1549 DCTN2 dynactin complex 50 kda subunit (50 kda dynein-associated polypeptide) (dynamitin) (dctn-50) (dynactin 2). [swissprot;acc:q13561] 225.159 1.01687 221.424
    SLMO1 erythroid differentiation and denucleation factor 1. [swissprot;acc:o60584] Subtracted 221.128 3.639 224.767
    1550 BBS7 bardet-biedl syndrome 7 protein isoform a; bbs2-like 1. [refseq;acc:nm_176824]
    SLC25A6 adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236] Divided 225.159 1.01687 221.424
    1551 no value ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] Subtracted 221.128 3.639 224.767
    SLC25A4 adp,atp carrier protein, heart/skeletal muscle isoform t1 (adp/atp translocase 1) (adenine nucleotide translocator 1) (ant 1). [swissprot;acc:p12235] Divided 225.159 1.01687 221.424
    1552 no value lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] Subtracted 221.128 3.639 224.767
    SLC25A5 adp,atp carrier protein, fibroblast isoform (adp/atp translocase 2) (adenine nucleotide translocator 2) (ant 2). [swissprot;acc:p05141] Divided 225.159 1.01687 221.424
    1553 AHCY adenosylhomocysteinase (ec 3.3.1.1) (s-adenosyl-l-homocysteine hydrolase) (adohcyase). [swissprot;acc:p23526] 215.389 1.01679 211.833
    SLMO2 protein c20orf45 (cgi-107). [swissprot;acc:q9y3b1] Subtracted 221.128 3.639 224.767
    1554 CTBP1 c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363] Divided 196.215 1.01656 193.018
    EIF3EIP eukaryotic translation initiation factor 3 subunit 6 interacting protein (hspc021/hspc025). [swissprot;acc:q9y262] Subtracted 221.128 3.639 224.767
    1555 PASK pas domain containing serine/threonine kinase; pas-serine/threonine kinase. [refseq;acc:nm_015148] Divided 196.192 1.01656 192.996
    RBM7 putative rna-binding protein 7 (rna binding motif protein 7). [swissprot;acc:q9y580] Subtracted 221.128 3.639 224.767
    1556 BCL6 b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [swissprot;acc:p41182] Divided 196.192 1.01656 192.996
    VARS valyl-trna synthetase 2 (ec 6.1.1.9) (valine--trna ligase 2) (valrs 2) (g7a). [swissprot;acc:p26640] Subtracted 223.589 3.63 227.219
    1557 AP1B1 adapter-related protein complex 1 beta 1 subunit (beta-adaptin 1) (adaptor protein complex ap-1 beta-1 subunit) (golgi adaptor ha1/ap1 adaptin beta subunit) (clathrin assembly protein complex 1 beta large chain). [swissprot;acc:q10567] 222.166 3.624 225.79
    SNAI2 zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623] Divided 196.192 1.01656 192.996
    1558 CTBP2 c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545] 196.171 1.01655 192.977
    FIP1L1 fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] Subtracted 115.817 3.615 119.432
    1559 BCL6B b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [refseq;acc:nm_181844] Divided 196.191 1.01655 192.996
    TMF1 tata element modulatory factor (tmf). [swissprot;acc:p82094] Subtracted 222.585 3.603 218.982
    1560 GATAD2A p66 alpha. [refseq;acc:nm_017660] Divided 167.687 1.01651 170.455
    SCYL1 scy1-like 1; telomerase regulation-associated protein; ht019 protein; telomerase regulation-associated protein; n-terminal kinase-like protein; teratoma-associated tyrosine kinase; n-terminal kinase-like. [refseq;acc:nm_020680] Subtracted 222.585 3.603 218.982
    1561 GATAD2B transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699] Divided 167.687 1.01651 170.455
    NUP98 nuclear pore complex protein nup98 (nucleoporin nup98) (98 kda nucleoporin). [swissprot;acc:p52948] Subtracted 222.585 3.603 218.982
    1562 no value tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] Divided 167.687 1.01651 170.455
    AMMECR1 ammecr1 protein. [refseq;acc:nm_015365] Subtracted 222.585 3.603 218.982

    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/