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 Network Comparison Type description Value Type Interaction Map Filtered red network_comparison green
    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
    		Hugo
    		description
    		red
    		network_comparison
    		green
    1562 no value tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] 167.687 1.01651 170.455
    1563 ATP5C1 atp synthase gamma chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p36542] 218.277 1.01648 214.739
    1564 ATP5O atp synthase oligomycin sensitivity conferral protein, mitochondrial precursor (ec 3.6.3.14) (oscp). [swissprot;acc:p48047]
    1565 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 1.01646 224.767
    1566 SLMO1 erythroid differentiation and denucleation factor 1. [swissprot;acc:o60584]
    1567 BBS7 bardet-biedl syndrome 7 protein isoform a; bbs2-like 1. [refseq;acc:nm_176824]
    1568 no value ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]
    1569 lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]
    1570 SLMO2 protein c20orf45 (cgi-107). [swissprot;acc:q9y3b1]
    1571 EIF3EIP eukaryotic translation initiation factor 3 subunit 6 interacting protein (hspc021/hspc025). [swissprot;acc:q9y262]
    1572 RBM7 putative rna-binding protein 7 (rna binding motif protein 7). [swissprot;acc:q9y580]
    1573 R3HDM1 r3h domain protein 1. [swissprot;acc:q15032] 218.105 214.573
    1574 TMF1 tata element modulatory factor (tmf). [swissprot;acc:p82094] 222.585 1.01645 218.982
    1575 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]
    1576 NUP98 nuclear pore complex protein nup98 (nucleoporin nup98) (98 kda nucleoporin). [swissprot;acc:p52948]
    1577 AMMECR1 ammecr1 protein. [refseq;acc:nm_015365]
    1578 RAE1 mrna-associated protein mrnp 41 (rae1 protein homolog). [swissprot;acc:p78406]
    1579 TATDN1 cda11 protein. [refseq;acc:nm_032026] 213.181 1.01644 209.732
    1580 CCNB2 g2/mitotic-specific cyclin b2. [swissprot;acc:o95067] 168.018 1.01637 170.769
    1581 CDK3 cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] 168.002 170.753
    1582 CCNB1 g2/mitotic-specific cyclin b1. [swissprot;acc:p14635] 168.098 1.01634 170.844
    1583 CDK2 cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941] 168.091 170.837
    1584 PGLS 6-phosphogluconolactonase (ec 3.1.1.31) (6pgl). [swissprot;acc:o95336] 216.891 1.01633 220.432
    1585 CDC2 cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493] 168.145 1.01631 170.888
    1586 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] 222.166 225.79
    1587 C20orf4 protein c20orf4 (protein cgi-23) (pro0225). [swissprot;acc:q9y312] 220.129 1.0163 216.598
    1588 RNF25 ring finger protein 25 (ec 6.3.2.-). [swissprot;acc:q96bh1] 177.834 1.01626 180.725
    1589 VARS valyl-trna synthetase 2 (ec 6.1.1.9) (valine--trna ligase 2) (valrs 2) (g7a). [swissprot;acc:p26640] 223.589 1.01624 227.219
    1590 TYMS thymidylate synthase (ec 2.1.1.45) (ts) (tsase). [swissprot;acc:p04818] 225.119 1.01621 228.769
    1591 no value dihydrofolate reductase (ec 1.5.1.3). [swissprot;acc:p00374]
    1592 SDF2 stromal cell-derived factor 2 precursor (sdf-2). [swissprot;acc:q99470]
    1593 SDF2L1 stromal cell-derived factor 2-like protein 1 precursor (sdf2 like protein 1) (pwp1-interacting protein 8). [swissprot;acc:q9hcn8]
    1594 JPH4 adapter-related protein complex 1 gamma 2 subunit (gamma2-adaptin) (adaptor protein complex ap-1 gamma-2 subunit) (g2ad). [swissprot;acc:o75843] 222.133 1.0162 225.731
    1595 no value 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] 222.134 1.01619
    1596 AP1G1 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]
    1597 AP1S3 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]
    1598 AP1S1 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]
    1599 DTNBP1 dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122] 217.871 1.01617 214.404
    1600 AP2B1 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] 222.103 1.01608 225.675
    1601 PMM2 phosphomannomutase 2 (ec 5.4.2.8) (pmm 2). [swissprot;acc:o15305] 217.268 1.01602 213.842
    1602 PMM1 phosphomannomutase 1 (ec 5.4.2.8) (pmm 1) (pmmh-22). [swissprot;acc:q92871] 217.334 1.01599 213.914
    1603 no value heat shock factor binding protein 1. [swissprot;acc:o75506] 216.62 1.01595 213.22
    1604 CLK2 protein kinase clk2 (ec 2.7.1.-) (cdc-like kinase 2). [swissprot;acc:p49760] 214.984 1.01593 211.614
    1605 FOXA1 hepatocyte nuclear factor 3-alpha (hnf-3a) (forkhead box protein a1). [swissprot;acc:p55317] 217.322 1.01592 213.916
    1606 APOA1BP apolipoprotein a-i binding protein; apoa-i binding protein. [refseq;acc:nm_144772] 207.916 1.0159 204.662
    1607 CLK3 protein kinase clk3 (ec 2.7.1.-) (cdc-like kinase 3). [swissprot;acc:p49761] 214.982 1.01588 211.622
    1608 TMEM189 ubiquitin-conjugating enzyme e2 variant 1 isoform b; dna-binding protein. [refseq;acc:nm_003349] 208.106 1.01581 204.867
    1609 UGP2 utp--glucose-1-phosphate uridylyltransferase 2 (ec 2.7.7.9) (udp- glucose pyrophosphorylase 2) (udpgp 2) (ugpase 2). [swissprot;acc:q16851] 208.113 1.0158 204.876
    1610 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] 208.122 1.01579 204.886
    1611 CEP70 p10-binding protein. [refseq;acc:nm_024491] 221.313 1.01577 217.877

    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/