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 [...,...].
    Gene Rank Hugo description Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 4208 to 4257 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		red
    		green
    		network_comparison
    1052 SERPINB8 plasminogen activator inhibitor-2 precursor (pai-2) (placental plasminogen activator inhibitor) (monocyte arg-serpin) (urokinase inhibitor). [swissprot;acc:p05120] Squared 20357.7 23353.8 1.14717
    1053 no value serpin b11. [swissprot;acc:q96p15]
    MPPED2 fetal brain protein 239 (239fb). [swissprot;acc:q15777] Measured 4757.46 5198.91 1.09279
    PSMA5 proteasome subunit alpha type 5 (ec 3.4.25.1) (proteasome zeta chain) (macropain zeta chain) (multicatalytic endopeptidase complex zeta chain). [swissprot;acc:p28066] Ranked 207.04 200.84 1.03087
    RANBP5 importin beta-3 subunit (karyopherin beta-3 subunit) (ran-binding protein 5). [swissprot;acc:o00410] Rooted 62.9727 66.1956 1.05118
    1054 no value 60s ribosomal protein l21. [swissprot;acc:p46778] Ranked 223.958 217.263 1.03082
    DLX3 homeobox protein dlx-3. [swissprot;acc:o60479] Measured 4757.46 5198.91 1.09279
    RANBP6 ran-gtp binding protein (fragment). [sptrembl;acc:o60518] Rooted 62.9646 66.1812 1.05109
    SERPINB6 placental thrombin inhibitor (cytoplasmic antiproteinase) (cap) (protease inhibitor 6) (pi-6). [swissprot;acc:p35237] Squared 20357.7 23353.8 1.14717
    1055 no value cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452]
    ASNSD1 hcv ns3-transactivated protein 1. [refseq;acc:nm_019048] Ranked 219.01 212.468 1.03079
    CSE1L importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [swissprot;acc:p55060] Rooted 74.1383 77.9257 1.05109
    TNK2 activated p21cdc42hs kinase. [refseq;acc:nm_005781] Measured 4757.46 5198.91 1.09279
    1056 ATP6V1A vacuolar atp synthase catalytic subunit a, ubiquitous isoform (ec 3.6.3.14) (v-atpase a subunit 1) (vacuolar proton pump alpha subunit 1) (v-atpase 69 kda subunit 1) (isoform va68). [swissprot;acc:p38606] Ranked 219.01 212.468 1.03079
    KIFC3 kinesin family member c3. [refseq;acc:nm_005550] Rooted 63.3481 66.5681 1.05083
    MAP3K7IP2 mitogen-activated protein kinase kinase kinase 7 interacting protein 2 isoform 1; tak1-binding protein 2. [refseq;acc:nm_015093] Measured 4757.46 5198.91 1.09279
    SERPINB1 leukocyte elastase inhibitor (lei) (monocyte/neutrophil elastase inhibitor) (m/nei) (ei). [swissprot;acc:p30740] Squared 20357.7 23353.8 1.14717
    1057 no value histone deacetylase 2 (hd2). [swissprot;acc:q92769] 28801.7 33039.9 1.14715
    ASNS asparagine synthetase [glutamine-hydrolyzing] (ec 6.3.5.4) (glutamine- dependent asparagine synthetase) (ts11 cell cycle control protein). [swissprot;acc:p08243] Ranked 219.01 212.468 1.03079
    DAZAP1 daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] Rooted 61.5291 64.6568 1.05083
    TMF1 tata element modulatory factor (tmf). [swissprot;acc:p82094] Measured 5412.23 5913.4 1.0926
    1058 ATXN2L ataxin 2 related protein isoform a; ataxin-2 domain protein. [refseq;acc:nm_007245] Ranked 228.105 221.293 1.03078
    MCFD2 multiple coagulation factor deficiency 2; neural stem cell derived neuronal survival protein; multiple coagulation factor deficiency protein 2. [refseq;acc:nm_139279] Squared 28801.2 33038.7 1.14713
    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] Measured 5412.23 5913.4 1.0926
    ZMIZ1 retinoic acid induced 17; pias-like protein hzimp10. [refseq;acc:nm_020338] Rooted 61.529 64.6562 1.05082
    1059 no value ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] Ranked 228.105 221.293 1.03078
    dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8] Squared 28801.2 33038.6 1.14713
    uridine kinase-like 1. [swissprot;acc:q9nwz5] Rooted 61.1919 64.2955 1.05072
    TBCC tubulin-specific chaperone c (tubulin-folding cofactor c) (cfc). [swissprot;acc:q15814] Measured 5719.01 6248.6 1.0926
    1060 ACOT9 putative acyl-coa thioester hydrolase cgi-16 (ec 3.1.2.-). [swissprot;acc:q9y305]
    HDAC1 histone deacetylase 1 (hd1). [swissprot;acc:q13547] Squared 28800.8 33037.5 1.1471
    NLK nemo-like kinase; likely ortholog of mouse nemo like kinase. [refseq;acc:nm_016231] Ranked 218.162 211.648 1.03078
    NME3 nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [swissprot;acc:q13232] Rooted 74.62 78.3934 1.05057
    1061 ERC1 elks protein. [refseq;acc:nm_015064] Ranked 218.162 211.648 1.03078
    HNRNPL heterogeneous nuclear ribonucleoprotein l (hnrnp l). [swissprot;acc:p14866] Squared 59335 68062.6 1.14709
    NME2P1 putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361] Rooted 73.8603 77.5904 1.0505
    NUP98 nuclear pore complex protein nup98 (nucleoporin nup98) (98 kda nucleoporin). [swissprot;acc:p52948] Measured 5412.23 5913.4 1.0926
    1062 AMMECR1 ammecr1 protein. [refseq;acc:nm_015365]
    NME2 nucleoside diphosphate kinase a (ec 2.7.4.6) (ndk a) (ndp kinase a) (tumor metastatic process-associated protein) (metastasis inhibition factor nm23) (nm23-h1). [swissprot;acc:p15531] Rooted 73.8553 77.585 1.0505
    RPP30 ribonuclease p protein subunit p30 (ec 3.1.26.5) (rnasep protein p30) (rnase p subunit 2). [swissprot;acc:p78346] Squared 17511.1 20085.3 1.147
    ZNF174 zinc finger protein 174 (aw-1). [swissprot;acc:q15697] Ranked 269.963 278.239 1.03066
    1063 no value nucleoside diphosphate kinase b (ec 2.7.4.6) (ndk b) (ndp kinase b) (nm23-h2) (c-myc purine-binding transcription factor puf). [swissprot;acc:p22392] Rooted 73.8426 77.5711 1.05049
    zinc finger imprinted 2. [swissprot;acc:q9nzv7] Ranked 269.96 278.232 1.03064
    PRKRAP1 protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] Squared 2709.8 3107.78 1.14687
    RAE1 mrna-associated protein mrnp 41 (rae1 protein homolog). [swissprot;acc:p78406] Measured 5412.23 5913.4 1.0926
    1064 no value transformer-2 protein homolog (tra-2 alpha). [swissprot;acc:q13595] Squared 31583.4 36221.8 1.14686
    DDX43 dead-box protein. [refseq;acc:nm_018665] Measured 5719.01 6248.6 1.0926
    TLE2 transducin-like enhancer protein 2 (esg2). [swissprot;acc:q04725] Rooted 63.2949 66.4799 1.05032
    ZNF24 zinc finger protein 24 (zinc finger protein 191) (zinc finger protein kox17) (retinoic acid suppression protein a) (rsg-a). [swissprot;acc:p17028] Ranked 269.955 278.221 1.03062
    1065 no value pepsin a precursor (ec 3.4.23.1). [swissprot;acc:p00790] Squared 17134.4 19648.7 1.14674

    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/