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 description Hugo Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 58974 to 59023 of 66312 in total
    Interaction Map  : Low confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Network Comparison Type
    		Value Type
    		red
    		green
    		network_comparison
    4144 syntaxin 6. [swissprot;acc:o43752] STX6 Divided Rooted 71.1775 73.0148 1.02581
    ubiquitin-conjugating enzyme e2-32 kda complementing (ec 6.3.2.19) (ubiquitin-protein ligase) (ubiquitin carrier protein) (e2-cdc34). [swissprot;acc:p49427] CDC34 Squared 41965.3 40878 1.0266
    zinnc finger protein gli4 (krueppel-related zinc finger protein 4) (hkr4 protein). [swissprot;acc:p10075] ZFP41 Subtracted Rooted 76.182 78.0463 1.8643
    4145 dead-box protein 3 (helicase-like protein 2) (hlp2) (dead-box, x isoform). [swissprot;acc:o00571] no value Squared 46040.5 44897.5 1143
    dihydrolipoamide dehydrogenase, mitochondrial precursor (ec 1.8.1.4) (glycine cleavage system l protein). [swissprot;acc:p09622] DLD Divided 45962 44773.1 1.02655
    protein x 0004. [refseq;acc:nm_016301] ATPBD1C Ranked 203.38 201.25 1.01058
    spermidine synthase (ec 2.5.1.16) (putrescine aminopropyltransferase) (spdsy). [swissprot;acc:p19623] SRM Rooted 75.6563 77.6088 1.02581
    transcription factor sp1. [swissprot;acc:p08047] no value Subtracted Measured 9146.05 9324.86 178.81
    trifunctional enzyme beta subunit, mitochondrial precursor (tp-beta) [includes: 3-ketoacyl-coa thiolase (ec 2.3.1.16) (acetyl-coa acyltransferase) (beta-ketothiolase)]. [swissprot;acc:p55084] HADHB Ranked 202.108 199.995 2.113
    tubulin-specific chaperone c (tubulin-folding cofactor c) (cfc). [swissprot;acc:q15814] TBCC Divided Measured 8065.14 8233.13 1.02083
    zinc finger protein 273 (zinc finger protein hzf9) (fragment). [swissprot;acc:q14593] no value Subtracted Rooted 76.1821 78.0464 1.8643
    4146 26s proteasome non-atpase regulatory subunit 4 (26s proteasome regulatory subunit s5a) (rpn10) (multiubiquitin chain binding protein) (antisecretory factor-1) (af) (asf). [swissprot;acc:p55036] PSMD4 Divided Squared 46086.4 44894.7 1.02654
    ca(2+)/calmodulin-dependent protein kinase phosphatase (ec 3.1.3.16) (cam-kinase phosphatase) (camkpase) (partner of pix 2) (hfem-2) (protein phosphatase 1f). [swissprot;acc:p49593] PPM1F Ranked 201.174 199.068 1.01058
    dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [refseq;acc:nm_139159] DPP9 Rooted 74.3444 76.2613 1.02578
    g1/s-specific cyclin e1. [swissprot;acc:p24864] CCNE1 Measured 8199.72 8370.36 1.02081
    hepatocyte nuclear factor 3-alpha (hnf-3a) (forkhead box protein a1). [swissprot;acc:p55317] FOXA1 Subtracted Ranked 205.411 203.301 2.11
    src homology 3 domain-containing protein hip-55. [refseq;acc:nm_014063] DBNL Squared 45807.8 44665 1142.8
    tubulin alpha-1 chain (alpha-tubulin 1). [swissprot;acc:p05209] TUBA1A Measured 8262.38 8083.7 178.68
    zinc finger protein 121 (zinc finger protein 20) (fragment). [swissprot;acc:p58317] no value Rooted 76.1821 78.0464 1.8643
    4147 actin, gamma-enteric smooth muscle (alpha-actin 3). [swissprot;acc:p12718] ACTG2 Measured 8073.12 8251.74 178.62
    fatty-acid amide hydrolase (ec 3.1.-.-) (oleamide hydrolase) (anandamide amidohydrolase). [swissprot;acc:o00519] FAAH Squared 46481.3 45339.6 1141.7
    homeobox protein dlx-2. [swissprot;acc:q07687] DLX2 Ranked 197.617 195.508 2.109
    nuclear pore complex protein nup155 (nucleoporin nup155) (155 kda nucleoporin). [swissprot;acc:o75694] NUP155 Divided Measured 8178.41 8348.47 1.02079
    nuclear pore complex protein nup214 (nucleoporin nup214) (214 kda nucleoporin) (can protein). [swissprot;acc:p35658] NUP214 Rooted 70.7752 72.5999 1.02578
    plasma membrane calcium-transporting atpase 3 (ec 3.6.3.8) (pmca3) (plasma membrane calcium pump isoform 3) (plasma membrane calcium atpase isoform 3). [swissprot;acc:q16720] ATP2B3 Ranked 201.079 198.973 1.01058
    sqv-7-like protein (fragment). [sptrembl;acc:o95454] SLC35D2 Squared 42071.7 40984.8 1.02652
    zinc finger protein 73 (zinc finger protein 186) (hznf2). [swissprot;acc:o43830] no value Subtracted Rooted 76.1821 78.0464 1.8643
    4148 actin, alpha cardiac. [swissprot;acc:p04270] ACTC1 Measured 8073.06 8251.68 178.62
    blocked early in transport 1 homolog (s. cerevisiae) like; golgi snare 15 kda protein. [refseq;acc:nm_016526] BET1L Squared 46839 47975.5 1136.5
    dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743] DPP8 Divided Rooted 74.3439 76.2606 1.02578
    fos-related antigen 1 (fra-1). [swissprot;acc:p15407] FOSL1 Squared 32529 33390.6 1.02649
    glyceraldehyde 3-phosphate dehydrogenase, liver (ec 1.2.1.12) (gapdh). [swissprot;acc:p04406] GAPDH Subtracted Ranked 200.477 198.368 2.109
    neuroserpin precursor (protease inhibitor 12). [swissprot;acc:q99574] SERPINI1 Divided Measured 8188.56 8358.68 1.02078
    plasma membrane calcium-transporting atpase 4 (ec 3.6.3.8) (pmca4) (plasma membrane calcium pump isoform 4) (plasma membrane calcium atpase isoform 4). [swissprot;acc:p23634] ATP2B4 Ranked 201.099 198.993 1.01058
    zinc finger protein 354b. [refseq;acc:nm_058230] ZNF354B Subtracted Rooted 76.1821 78.0464 1.8643
    4149 60s ribosomal protein l9, mitochondrial precursor (l9mt). [swissprot;acc:q9byd2] MRPL9 Divided Measured 8188.56 8358.68 1.02078
    actin, aortic smooth muscle (alpha-actin 2). [swissprot;acc:p03996] ACTA2 Subtracted 8073.12 8251.74 178.62
    adp-ribosylation factor guanine nucleotide factor 6; hepatocellular carcinoma-associated antigen 67. [refseq;acc:nm_015310] PSD3 Divided Ranked 200.724 198.625 1.01057
    human immunodeficiency virus type i enhancer binding protein 3. [refseq;acc:nm_024503] HIVEP3 Rooted 75.0999 77.0351 1.02577
    oxidation resistance 1. [refseq;acc:nm_181354] OXR1 Subtracted Ranked 200.018 197.911 2.107
    peroxisome assembly factor-1 (paf-1) (peroxin-2) (peroxisomal membrane protein 3) (35 kda peroxisomal membrane protein). [swissprot;acc:p28328] PXMP3 Divided Squared 42606.3 41507.2 1.02648
    tryptophanyl-trna synthetase, mitochondrial precursor (ec 6.1.1.2) (tryptophan--trna ligase) (trprs) ((mt)trprs). [swissprot;acc:q9ugm6] WARS2 Subtracted 43125.1 41990.2 1134.9
    zinc finger protein 454. [refseq;acc:nm_182594] ZNF454 Rooted 76.1821 78.0464 1.8643
    4150 14.5 kda translational inhibitor protein (p14.5) (uk114 antigen homolog). [swissprot;acc:p52758] HRSP12 Divided Squared 45383.4 44213.2 1.02647
    ezrin (p81) (cytovillin) (villin 2). [swissprot;acc:p15311] VIL2 Subtracted 44419.9 43285.6 1134.3
    numb-like protein (numb-r). [swissprot;acc:q9y6r0] NUMBL Divided Rooted 70.7643 72.5856 1.02574
    plasma membrane calcium-transporting atpase 2 (ec 3.6.3.8) (pmca2) (plasma membrane calcium pump isoform 2) (plasma membrane calcium atpase isoform 2). [swissprot;acc:q01814] ATP2B2 Subtracted Ranked 201.107 199 2.107
    putative membrane protein. [refseq;acc:nm_019026] TMCO1 Divided Measured 8188.56 8358.68 1.02078
    pyruvate dehydrogenase e1 component beta subunit, mitochondrial precursor (ec 1.2.4.1) (pdhe1-b). [swissprot;acc:p11177] PDHB Subtracted 8222.64 8401.15 178.51
    trs85 homolog. [swissprot;acc:q9y2l5] KIAA1012 Divided Ranked 200.724 198.625 1.01057

    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/