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 Network Comparison Type Hugo Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1562 to 1611 of 3228 in total
    Network Comparison Type  : Divided
    Value Type  : Ranked
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		red
    		green
    		network_comparison
    1562 tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] no value 167.687 170.455 1.01651
    1563 atp synthase gamma chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p36542] ATP5C1 218.277 214.739 1.01648
    1564 atp synthase oligomycin sensitivity conferral protein, mitochondrial precursor (ec 3.6.3.14) (oscp). [swissprot;acc:p48047] ATP5O
    1565 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 1.01646
    1566 erythroid differentiation and denucleation factor 1. [swissprot;acc:o60584] SLMO1
    1567 bardet-biedl syndrome 7 protein isoform a; bbs2-like 1. [refseq;acc:nm_176824] BBS7
    1568 ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] no value
    1569 lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]
    1570 protein c20orf45 (cgi-107). [swissprot;acc:q9y3b1] SLMO2
    1571 eukaryotic translation initiation factor 3 subunit 6 interacting protein (hspc021/hspc025). [swissprot;acc:q9y262] EIF3EIP
    1572 putative rna-binding protein 7 (rna binding motif protein 7). [swissprot;acc:q9y580] RBM7
    1573 r3h domain protein 1. [swissprot;acc:q15032] R3HDM1 218.105 214.573
    1574 tata element modulatory factor (tmf). [swissprot;acc:p82094] TMF1 222.585 218.982 1.01645
    1575 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] SCYL1
    1576 nuclear pore complex protein nup98 (nucleoporin nup98) (98 kda nucleoporin). [swissprot;acc:p52948] NUP98
    1577 ammecr1 protein. [refseq;acc:nm_015365] AMMECR1
    1578 mrna-associated protein mrnp 41 (rae1 protein homolog). [swissprot;acc:p78406] RAE1
    1579 cda11 protein. [refseq;acc:nm_032026] TATDN1 213.181 209.732 1.01644
    1580 g2/mitotic-specific cyclin b2. [swissprot;acc:o95067] CCNB2 168.018 170.769 1.01637
    1581 cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] CDK3 168.002 170.753
    1582 g2/mitotic-specific cyclin b1. [swissprot;acc:p14635] CCNB1 168.098 170.844 1.01634
    1583 cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941] CDK2 168.091 170.837
    1584 6-phosphogluconolactonase (ec 3.1.1.31) (6pgl). [swissprot;acc:o95336] PGLS 216.891 220.432 1.01633
    1585 cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493] CDC2 168.145 170.888 1.01631
    1586 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] AP1B1 222.166 225.79
    1587 protein c20orf4 (protein cgi-23) (pro0225). [swissprot;acc:q9y312] C20orf4 220.129 216.598 1.0163
    1588 ring finger protein 25 (ec 6.3.2.-). [swissprot;acc:q96bh1] RNF25 177.834 180.725 1.01626
    1589 valyl-trna synthetase 2 (ec 6.1.1.9) (valine--trna ligase 2) (valrs 2) (g7a). [swissprot;acc:p26640] VARS 223.589 227.219 1.01624
    1590 thymidylate synthase (ec 2.1.1.45) (ts) (tsase). [swissprot;acc:p04818] TYMS 225.119 228.769 1.01621
    1591 dihydrofolate reductase (ec 1.5.1.3). [swissprot;acc:p00374] no value
    1592 stromal cell-derived factor 2 precursor (sdf-2). [swissprot;acc:q99470] SDF2
    1593 stromal cell-derived factor 2-like protein 1 precursor (sdf2 like protein 1) (pwp1-interacting protein 8). [swissprot;acc:q9hcn8] SDF2L1
    1594 adapter-related protein complex 1 gamma 2 subunit (gamma2-adaptin) (adaptor protein complex ap-1 gamma-2 subunit) (g2ad). [swissprot;acc:o75843] JPH4 222.133 225.731 1.0162
    1595 adapter-related protein complex 1 sigma 1b subunit (sigma-adaptin 1b) (adaptor protein complex ap-1 sigma-1b subunit) (golgi adaptor ha1/ap1 adaptin sigma-1b subunit) (clathrin assembly protein complex 1 sigma- 1b small chain) (sigma 1b subunit of ap-1 clathrin) (dc22). [swissprot;acc:p56377] no value 222.134 1.01619
    1596 adapter-related protein complex 1 gamma 1 subunit (gamma-adaptin) (adaptor protein complex ap-1 gamma-1 subunit) (golgi adaptor ha1/ap1 adaptin gamma-1 subunit) (clathrin assembly protein complex 1 gamma-1 large chain). [swissprot;acc:o43747] AP1G1
    1597 adapter-related protein complex 1 sigma 1c subunit (sigma-adaptin 1c) (adaptor protein complex ap-1 sigma-1c subunit) (golgi adaptor ha1/ap1 adaptin sigma-1c subunit) (clathrin assembly protein complex 1 sigma- 1c small chain) (sigma 1c subunit of ap-1 clathrin). [swissprot;acc:q96pc3] AP1S3
    1598 adapter-related protein complex 1 sigma 1a subunit (sigma-adaptin 1a) (adaptor protein complex ap-1 sigma-1a subunit) (golgi adaptor ha1/ap1 adaptin sigma-1a subunit) (clathrin assembly protein complex 1 sigma- 1a small chain) (clathrin coat assembly protein ap19) (ha1 19 kda subunit) (sigma 1a subunit of ap-1 clathrin). [swissprot;acc:q00382] AP1S1
    1599 dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122] DTNBP1 217.871 214.404 1.01617
    1600 adapter-related protein complex 2 beta 1 subunit (beta-adaptin) (plasma membrane adaptor ha2/ap2 adaptin beta subunit) (clathrin assembly protein complex 2 beta large chain) (ap105b). [swissprot;acc:p21851] AP2B1 222.103 225.675 1.01608
    1601 phosphomannomutase 2 (ec 5.4.2.8) (pmm 2). [swissprot;acc:o15305] PMM2 217.268 213.842 1.01602
    1602 phosphomannomutase 1 (ec 5.4.2.8) (pmm 1) (pmmh-22). [swissprot;acc:q92871] PMM1 217.334 213.914 1.01599
    1603 heat shock factor binding protein 1. [swissprot;acc:o75506] no value 216.62 213.22 1.01595
    1604 protein kinase clk2 (ec 2.7.1.-) (cdc-like kinase 2). [swissprot;acc:p49760] CLK2 214.984 211.614 1.01593
    1605 hepatocyte nuclear factor 3-alpha (hnf-3a) (forkhead box protein a1). [swissprot;acc:p55317] FOXA1 217.322 213.916 1.01592
    1606 apolipoprotein a-i binding protein; apoa-i binding protein. [refseq;acc:nm_144772] APOA1BP 207.916 204.662 1.0159
    1607 protein kinase clk3 (ec 2.7.1.-) (cdc-like kinase 3). [swissprot;acc:p49761] CLK3 214.982 211.622 1.01588
    1608 ubiquitin-conjugating enzyme e2 variant 1 isoform b; dna-binding protein. [refseq;acc:nm_003349] TMEM189 208.106 204.867 1.01581
    1609 utp--glucose-1-phosphate uridylyltransferase 2 (ec 2.7.7.9) (udp- glucose pyrophosphorylase 2) (udpgp 2) (ugpase 2). [swissprot;acc:q16851] UGP2 208.113 204.876 1.0158
    1610 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] UBE2V2 208.122 204.886 1.01579
    1611 p10-binding protein. [refseq;acc:nm_024491] CEP70 221.313 217.877 1.01577

    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/