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 2964 to 3013 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		red
    		green
    		network_comparison
    741 SNW1 nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573] Squared 23894.7 27894.5 1.16739
    742 BRP44 brain protein 44. [swissprot;acc:o95563] Ranked 126.215 120.078 1.05111
    BTF3 transcription factor btf3 (rna polymerase b transcription factor 3). [swissprot;acc:p20290] Rooted 67.0234 71.5506 1.06755
    EIF3G eukaryotic translation initiation factor 3 subunit 4 (eif-3 delta) (eif3 p44) (eif-3 rna-binding subunit) (eif3 p42) (eif3g). [swissprot;acc:o75821] Measured 4131.04 4607.9 1.11543
    EN2 homeobox protein engrailed-2 (hu-en-2). [swissprot;acc:p19622] Squared 31406.6 36662.8 1.16736
    743 CXXC1 cpg binding protein (protein containing phd finger and cxxc domain 1). [swissprot;acc:q9p0u4]
    EIF3A eukaryotic translation initiation factor 3 subunit 10 (eif-3 theta) (eif3 p167) (eif3 p180) (eif3 p185) (eif3a). [swissprot;acc:q14152] Measured 4131.04 4607.9 1.11543
    KATNA1 katanin p60 subunit a 1. [refseq;acc:nm_007044] Rooted 54.4988 51.0573 1.0674
    SEPT7 septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] Ranked 126.215 120.078 1.05111
    744 ABT1 activator of basal transcription 1; tata-binding protein-binding protein; basal transcriptional activator. [refseq;acc:nm_013375] Squared 31406.6 36662.8 1.16736
    CTPS2 cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857] Measured 12515.4 11221.1 1.11535
    DCTN5 dynactin 4. [refseq;acc:nm_032486] Rooted 55.2242 51.7372 1.0674
    SEPT6 septin 6. [swissprot;acc:q14141] Ranked 126.604 120.463 1.05098
    745 no value cytokine-like nuclear factor n-pac. [refseq;acc:nm_032569] Squared 31406.6 36662.8 1.16736
    transcription factor btf3 homolog 3. [swissprot;acc:q13892] Rooted 67.0475 71.5566 1.06725
    NET1 neuroepithelial cell transforming gene 1; guanine nucleotide regulatory protein (oncogene); rho guanine nucleotide exchange factor (gef) 8. [refseq;acc:nm_005863] Measured 4086.6 4557.68 1.11527
    SLC35B1 solute carrier family 35, member b1; udp-galactose transporter related. [refseq;acc:nm_005827] Ranked 214.679 225.568 1.05072
    746 ARHGEF3 rho guanine nucleotide exchange factor 3; rhogef protein; 59.8 kda protein; exchange factor found in platelets and leukemic and neuronal tissues, xpln. [refseq;acc:nm_019555] Measured 4086.6 4557.68 1.11527
    EIF3I eukaryotic translation initiation factor 3 subunit 2 (eif-3 beta) (eif3 p36) (eif3i) (tgf-beta receptor interacting protein 1) (trip-1). [swissprot;acc:q13347] Ranked 250.465 238.38 1.0507
    HECW1 hect type e3 ubiquitin ligase. [refseq;acc:nm_015052] Squared 31406.6 36662.8 1.16736
    KATNB1 katanin p80 subunit b 1; katanin (80 kda); katanin p80 (wd40-containing) subunit b 1. [refseq;acc:nm_005886] Rooted 54.5195 51.084 1.06725
    747 no value trinucleotide repeat containing 15. [refseq;acc:nm_015575] Ranked 250.465 238.38 1.0507
    SFRS18 sr rich protein. [refseq;acc:nm_032870] Rooted 61.4809 65.6088 1.06714
    TLE3 transducin-like enhancer protein 3 (esg3). [swissprot;acc:q04726] Squared 31401.8 36655.7 1.16731
    UTP20 down-regulated in metastasis. [refseq;acc:nm_014503] Measured 4086.6 4557.68 1.11527
    748 BCAS2 breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872] Squared 23148.8 27021.5 1.1673
    CTPS ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812] Measured 12503.3 11212 1.11517
    FBL fibrillarin (34 kda nucleolar scleroderma antigen). [swissprot;acc:p22087] Ranked 245.246 233.483 1.05038
    PMPCB mitochondrial processing peptidase beta subunit, mitochondrial precursor (ec 3.4.24.64) (beta-mpp) (p-52). [swissprot;acc:o75439] Rooted 60.4376 64.4898 1.06705
    749 CDC5L cdc5-like; cdc5 (cell division cycle 5, s. pombe, homolog)-like; cell division cycle 5, s. pombe, homolog-like; cdc5-related protein. [refseq;acc:nm_001253] Squared 23148.8 27021.5 1.1673
    EXOC6B exocyst complex component sec15b. [swissprot;acc:q9y2d4] Ranked 221.968 211.326 1.05036
    PCYT2 ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [swissprot;acc:q99447] Measured 4565.34 5085.92 1.11403
    PRKAG1 5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619] Rooted 66.9737 71.4637 1.06704
    750 EXOC6 exocyst complex component sec15a. [swissprot;acc:q8tag9] Ranked 222.138 211.503 1.05028
    MYL1 myosin light chain 1, skeletal muscle isoform (mlc1f) (a1 catalytic) (alkali). [swissprot;acc:p05976] Measured 4565.34 5085.92 1.11403
    NAT5 n-acetyltransferase 5 (ec 2.3.1.-). [swissprot;acc:q9y6d2] Squared 21678.4 25303.3 1.16721
    PMPCA mitochondrial processing peptidase alpha subunit, mitochondrial precursor (ec 3.4.24.64) (alpha-mpp) (p-55) (ha1523). [swissprot;acc:q10713] Rooted 60.4385 64.49 1.06704
    751 no value ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] Squared 20305.9 23689.4 1.16663
    u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695] Ranked 223.463 212.875 1.04974
    MYL3 myosin light chain 1, slow-twitch muscle b/ventricular isoform (mlc1sb) (alkali). [swissprot;acc:p08590] Measured 4565.34 5085.92 1.11403
    PRKAA2 5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646] Rooted 66.9738 71.4638 1.06704
    752 NDUFS6 nadh-ubiquinone oxidoreductase 13 kda-a subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-a) (ci-13kd-a). [swissprot;acc:o75380] Measured 4565.34 5085.92 1.11403
    PRKAA1 5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131] Rooted 66.9736 71.4636 1.06704
    SLU7 step ii splicing factor slu7. [refseq;acc:nm_006425] Ranked 223.463 212.875 1.04974
    SNRPA1 u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661] Squared 20305.9 23689.4 1.16663
    753 HLCS biotin--protein ligase (ec 6.3.4.-) (biotin apo-protein ligase) [includes: biotin--[methylmalonyl-coa-carboxyltransferase] ligase (ec 6.3.4.9); biotin--[propionyl-coa-carboxylase [atp-hydrolyzing]] ligase (ec 6.3.4.10) (holocarboxylase synthetase) (hcs); biotin--[methylcrotonoyl-coa-carboxylase] ligase (ec 6.3.4.11); biotin--[acetyl-coa-carboxylase] ligase (ec 6.3.4.15)]. [swissprot;acc:p50747] 24183.6 28211.1 1.16654
    LBP lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428] Ranked 224.434 235.583 1.04968
    MYL6 myosin light chain 1, slow-twitch muscle a isoform (mlc1sa) (alkali). [swissprot;acc:p14649] Measured 4565.34 5085.92 1.11403
    PRKAB2 5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741] Rooted 66.9737 71.4637 1.06704
    754 no value myosin light chain 1, embryonic muscle/atrial isoform (pro1957). [swissprot;acc:p12829] Measured 4565.34 5085.92 1.11403

    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/