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 Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 8141 to 8190 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		red
    		green
    		network_comparison
    2036 ATP5J2 atp synthase f chain, mitochondrial (ec 3.6.3.14). [swissprot;acc:p56134] Measured 6920.71 7315.59 1.05706
    HRSP12 14.5 kda translational inhibitor protein (p14.5) (uk114 antigen homolog). [swissprot;acc:p52758] Rooted 66.966 68.7832 1.02714
    LMNB1 lamin b1. [swissprot;acc:p20700] Ranked 218.919 220.813 1.00865
    WWTR1 transcriptional co-activator with pdz-binding motif (taz). [refseq;acc:nm_015472] Squared 25972.4 28319.2 1.09036
    2037 CENTB1 centaurin beta 1 (cnt-b1). [swissprot;acc:q15027] Ranked 218.919 220.812 1.00865
    DHX35 probable atp-dependent helicase ddx35 (deah-box protein 35). [swissprot;acc:q9h5z1] Measured 6920.71 7315.59 1.05706
    HSP90AA2 heat shock protein hsp 90-alpha (hsp 86). [swissprot;acc:p07900] Rooted 61.2508 62.9087 1.02707
    RCAN2 calcipressin 2 (thyroid hormone-responsive protein zaki-4) (down syndrome candidate region 1-like 1) (myocyte-enriched calcineurin interacting protein 2) (mcip2). [swissprot;acc:q14206] Squared 24791.2 27031.1 1.09035
    2038 COL4A3 collagen alpha 3(iv) chain precursor (goodpasture antigen). [swissprot;acc:q01955] 25972.3 28319
    LMNA lamin a/c (70 kda lamin). [swissprot;acc:p02545] Ranked 218.92 220.811 1.00864
    PSMD13 26s proteasome non-atpase regulatory subunit 13 (26s proteasome regulatory subunit s11) (26s proteasome regulatory subunit p40.5). [swissprot;acc:q9unm6] Rooted 62.382 64.07 1.02706
    TAF6 transcription initiation factor tfiid 70 kda subunit (tafii-70) (tafii-80) (tafii80). [swissprot;acc:p49848] Measured 7088.08 7492.23 1.05702
    2039 ACSS2 acetyl-coenzyme a synthetase, cytoplasmic (ec 6.2.1.1) (acetate--coa ligase) (acyl-activating enzyme) (acetyl-coa synthetase) (acs) (acecs). [swissprot;acc:q9nr19] Ranked 190.551 192.191 1.00861
    MRPL4 mitochondrial ribosomal protein l4 isoform a. [refseq;acc:nm_015956] Measured 3646.01 3449.54 1.05696
    RCAN3 calcipressin 3 (down syndrome candidate region 1-like protein 2) (myocyte-enriched calcineurin interacting protein 3) (mcip3). [swissprot;acc:q9uka8] Squared 24791.2 27031.1 1.09035
    SUMO1P3 ubiquitin-like protein smt3c precursor (ubiquitin-homology domain protein pic1) (ubiquitin-like protein ubl1) (ubiquitin-related protein sumo-1) (gap modifying protein 1) (gmp1) (sentrin). [swissprot;acc:q93068] Rooted 62.5393 64.227 1.02699
    2040 LDB3 zasp protein (fragment). [sptrembl;acc:q9y4z3] Squared 25972 28318 1.09033
    PRR5 rho-gtpase-activating protein 8. [swissprot;acc:q9nsg0] Measured 6036.68 6379.44 1.05678
    T brachyury protein (t protein). [swissprot;acc:o15178] Ranked 210.586 208.803 1.00854
    UGDH udp-glucose 6-dehydrogenase (ec 1.1.1.22) (udp-glc dehydrogenase) (udp-glcdh) (udpgdh). [swissprot;acc:o60701] Rooted 62.5393 64.227 1.02699
    2041 no value 60s ribosomal protein l9. [swissprot;acc:p32969] Squared 13232.9 14427.3 1.09026
    ARHGAP1 rho-gtpase-activating protein 1 (gtpase-activating protein rhoogap) (rho-related small gtpase protein activator) (cdc42 gtpase-activating protein) (p50-rhogap). [swissprot;acc:q07960] Measured 6036.68 6379.44 1.05678
    PGD 6-phosphogluconate dehydrogenase, decarboxylating (ec 1.1.1.44). [swissprot;acc:p52209] Rooted 63.5421 65.2562 1.02698
    UBQLN4 ataxin-1 ubiquitin-like interacting protein. [refseq;acc:nm_020131] Ranked 196.808 195.141 1.00854
    2042 BRPF1 tubulin tyrosine ligase-like protein hottl (hqp0207). [swissprot;acc:q9y4r7] Rooted 59.4136 61.0113 1.02689
    KLC2 kinesin light chain 2 (klc 2). [swissprot;acc:q9h0b6] Measured 6036.62 6379.38 1.05678
    PRKAR2A camp-dependent protein kinase type ii-alpha regulatory chain. [swissprot;acc:p13861] Squared 26513.8 28905.8 1.09022
    TBX19 t-box transcription factor tbx19 (t-box protein 19). [swissprot;acc:o60806] Ranked 210.586 208.803 1.00854
    2043 KIF5B kinesin heavy chain (ubiquitous kinesin heavy chain) (ukhc). [swissprot;acc:p33176] Measured 6036.68 6379.44 1.05678
    PRKX protein kinase pkx1 (ec 2.7.1.-). [swissprot;acc:p51817] Squared 26521.7 28913.2 1.09017
    TXNIP thioredoxin interacting protein; upregulated by 1,25-dihydroxyvitamin d-3. [refseq;acc:nm_006472] Rooted 60.9498 62.5881 1.02688
    UBQLN1 ubiquilin 1 isoform 1. [refseq;acc:nm_013438] Ranked 196.837 195.173 1.00853
    2044 AP3B1 adapter-related protein complex 3 beta 1 subunit (beta-adaptin 3a) (ap-3 complex beta-3a subunit) (beta-3a-adaptin). [swissprot;acc:o00203] 199.928 198.24 1.00851
    KIF5C kinesin heavy chain isoform 5c (kinesin heavy chain neuron-specific 2). [swissprot;acc:o60282] Measured 6036.68 6379.44 1.05678
    PRKACG camp-dependent protein kinase, gamma-catalytic subunit (ec 2.7.1.37) (pka c-gamma). [swissprot;acc:p22612] Squared 26521.7 28913.2 1.09017
    PSMC4 26s protease regulatory subunit 6b (mip224) (mb67 interacting protein) (tat-binding protein-7) (tbp-7). [swissprot;acc:p43686] Rooted 62.2342 63.9055 1.02686
    2045 no value 26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232] 62.309 63.9809 1.02683
    C19orf29 ny-ren-24 antigen (fragment). [sptrembl;acc:q9y5a4] Ranked 199.928 198.24 1.00851
    KIF5A neuronal kinesin heavy chain (nkhc) (kinesin heavy chain isoform 5a) (kinesin heavy chain neuron-specific 1). [swissprot;acc:q12840] Measured 6036.68 6379.44 1.05678
    PRKACB camp-dependent protein kinase, beta-catalytic subunit (ec 2.7.1.37) (pka c-beta). [swissprot;acc:p22694] Squared 26521.7 28913.2 1.09017
    2046 no value adapter-related protein complex 3 beta 2 subunit (beta-adaptin 3b) (ap-3 complex beta-3b subunit) (beta-3b-adaptin) (neuron-specific vesicle coat protein beta-nap). [swissprot;acc:q13367] Ranked 199.928 198.24 1.00851
    ASL argininosuccinate lyase (ec 4.3.2.1) (arginosuccinase) (asal). [swissprot;acc:p04424] Rooted 62.6557 64.3308 1.02673
    KLC1 kinesin light chain 1 (klc 1). [swissprot;acc:q07866] Measured 6036.73 6379.48 1.05678
    PRKACA camp-dependent protein kinase, alpha-catalytic subunit (ec 2.7.1.37) (pka c-alpha). [swissprot;acc:p17612] Squared 26521.7 28913.2 1.09017
    2047 EPN2 epsin 2 isoform b; eps15 binding protein. [refseq;acc:nm_014964] Rooted 62.5767 64.2492 1.02673
    GTF3A transcription factor iiia (factor a) (tfiiia). [swissprot;acc:q92664] Measured 6036.68 6379.44 1.05678
    PRKAR2B camp-dependent protein kinase type ii-beta regulatory chain. [swissprot;acc:p31323] Squared 26530.8 28921.7 1.09012
    SLC2A6 solute carrier family 2, facilitated glucose transporter, member 6 (glucose transporter type 6) (glucose transporter type 9). [swissprot;acc:q9ugq3] Ranked 224.124 226.003 1.00838
    2048 CFL1 cofilin, non-muscle isoform (18 kda phosphoprotein) (p18). [swissprot;acc:p23528] Squared 30902.9 33687.7 1.09011
    EXOC1 exocyst complex component sec3 (bm-012). [swissprot;acc:q9nv70] Measured 6036.68 6379.44 1.05678

    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/