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 Hugo Value Type Gene description Interaction Map Network Comparison Type Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1551 to 1600 of 3228 in total
    Value Type  : Ranked
    Interaction Map  : High confidence
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Hugo
    		description
    		red
    		green
    		network_comparison
    1551 SLC25A4 adp,atp carrier protein, heart/skeletal muscle isoform t1 (adp/atp translocase 1) (adenine nucleotide translocator 1) (ant 1). [swissprot;acc:p12235] 225.159 221.424 1.01687
    1552 SLC25A5 adp,atp carrier protein, fibroblast isoform (adp/atp translocase 2) (adenine nucleotide translocator 2) (ant 2). [swissprot;acc:p05141]
    1553 AHCY adenosylhomocysteinase (ec 3.3.1.1) (s-adenosyl-l-homocysteine hydrolase) (adohcyase). [swissprot;acc:p23526] 215.389 211.833 1.01679
    1554 CTBP1 c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363] 196.215 193.018 1.01656
    1555 PASK pas domain containing serine/threonine kinase; pas-serine/threonine kinase. [refseq;acc:nm_015148] 196.192 192.996
    1556 BCL6 b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [swissprot;acc:p41182]
    1557 SNAI2 zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623]
    1558 CTBP2 c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545] 196.171 192.977 1.01655
    1559 BCL6B b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [refseq;acc:nm_181844] 196.191 192.996
    1560 GATAD2A p66 alpha. [refseq;acc:nm_017660] 167.687 170.455 1.01651
    1561 GATAD2B transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699]
    1562 no value tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735]
    1563 ATP5C1 atp synthase gamma chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p36542] 218.277 214.739 1.01648
    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] 221.128 224.767 1.01646
    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] 222.585 218.982 1.01645
    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] 213.181 209.732 1.01644
    1580 CCNB2 g2/mitotic-specific cyclin b2. [swissprot;acc:o95067] 168.018 170.769 1.01637
    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] 168.098 170.844 1.01634
    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] 216.891 220.432 1.01633
    1585 CDC2 cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493] 168.145 170.888 1.01631
    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] 220.129 216.598 1.0163
    1588 RNF25 ring finger protein 25 (ec 6.3.2.-). [swissprot;acc:q96bh1] 177.834 180.725 1.01626
    1589 VARS valyl-trna synthetase 2 (ec 6.1.1.9) (valine--trna ligase 2) (valrs 2) (g7a). [swissprot;acc:p26640] 223.589 227.219 1.01624
    1590 TYMS thymidylate synthase (ec 2.1.1.45) (ts) (tsase). [swissprot;acc:p04818] 225.119 228.769 1.01621
    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] 222.133 225.731 1.0162
    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] 217.871 214.404 1.01617
    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] 222.103 225.675 1.01608

    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/