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 [...,...].
    description Rank Gene Value Type Network Comparison Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 951 to 1000 of 3228 in total
    Value Type  : Measured
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    description
    		Rank
    		red
    		network_comparison
    		green
    epsin 3. [refseq;acc:nm_017957] 1809 5816.12 1.06535 6196.21
    ergic-53 protein precursor (er-golgi intermediate compartment 53 kda protein) (lectin, mannose-binding 1) (gp58) (intracellular mannose specific lectin mr60). [swissprot;acc:p49257] 3177 0.00001 1 0.00001
    ero1-like. [refseq;acc:nm_014584] 855 6562.98 1.10352 7242.37
    erythroid differentiation and denucleation factor 1. [swissprot;acc:o60584] 2128 5328.73 1.05402 5616.59
    erythroid differentiation-related factor 1. [refseq;acc:nm_015608] 3095 0.00001 1 0.00001
    espin. [refseq;acc:nm_031475] 1876 6076.66 1.0636 6463.12
    esterase d (ec 3.1.1.1). [swissprot;acc:p10768] 2250 6834.03 1.04677 7153.66
    estradiol 17 beta-dehydrogenase 1 (ec 1.1.1.62) (17-beta-hsd 1) (placental 17-beta-hydroxysteroid dehydrogenase) (20 alpha- hydroxysteroid dehydrogenase) (20-alpha-hsd) (e2dh). [swissprot;acc:p14061] 2520 5964.17 1.02511 6113.96
    estradiol 17 beta-dehydrogenase 4 (ec 1.1.1.62) (17-beta-hsd 4) (17-beta-hydroxysteroid dehydrogenase 4). [swissprot;acc:p51659] 2538 7121.07 1.02325 7286.61
    estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454] 902 10246.1 1.10147 11285.8
    ethanolamine kinase (ec 2.7.1.82) (eki). [swissprot;acc:q9hbu6] 2328 6773.67 1.04456 7075.51
    ethanolamine kinase-like protein eki2 (flj10761). [swissprot;acc:q9nvf9] 2327
    ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [swissprot;acc:q99447] 749 4565.34 1.11403 5085.92
    eukaryotic initiation factor 4a-i (eif-4a-i) (eif4a-i). [swissprot;acc:p04765] 2868 0.00001 1 0.00001
    eukaryotic initiation factor 4a-ii (eif-4a-ii) (eif4a-ii). [swissprot;acc:q14240] 2888
    eukaryotic peptide chain release factor subunit 1 (erf1) (eukaryotic release factor 1) (tb3-1) (c11 protein). [swissprot;acc:p46055] 2621 5599.85 1.01485 5683
    eukaryotic translation initiation factor 2 subunit 1 (eukaryotic translation initiation factor 2 alpha subunit) (eif-2-alpha) (eif- 2alpha) (eif-2a). [swissprot;acc:p05198] 2031 5060.82 1.05732 5350.93
    eukaryotic translation initiation factor 2 subunit 2 (eukaryotic translation initiation factor 2 beta subunit) (eif-2-beta). [swissprot;acc:p20042] 1753 5423.67 1.06707 5787.46
    eukaryotic translation initiation factor 2 subunit 3 (eukaryotic translation initiation factor 2 gamma subunit) (eif-2-gamma). [swissprot;acc:p41091] 1882 5490.24 1.06346 5838.67
    eukaryotic translation initiation factor 3 subunit 10 (eif-3 theta) (eif3 p167) (eif3 p180) (eif3 p185) (eif3a). [swissprot;acc:q14152] 743 4131.04 1.11543 4607.9
    eukaryotic translation initiation factor 3 subunit 11 (eif-3 p25) (eif3k) (muscle specific gene m9 protein) (ptd001) (hspc029) (arg134). [swissprot;acc:q9ubq5] 2127 5328.73 1.05402 5616.59
    eukaryotic translation initiation factor 3 subunit 2 (eif-3 beta) (eif3 p36) (eif3i) (tgf-beta receptor interacting protein 1) (trip-1). [swissprot;acc:q13347] 612 3975.77 1.1281 4485.05
    eukaryotic translation initiation factor 3 subunit 4 (eif-3 delta) (eif3 p44) (eif-3 rna-binding subunit) (eif3 p42) (eif3g). [swissprot;acc:o75821] 742 4131.04 1.11543 4607.9
    eukaryotic translation initiation factor 3 subunit 6 interacting protein (hspc021/hspc025). [swissprot;acc:q9y262] 2133 5328.73 1.05402 5616.59
    eukaryotic translation initiation factor 3 subunit 7 (eif-3 zeta) (eif3 p66) (eif3d). [swissprot;acc:o15371] 1597 5665.34 1.07148 6070.32
    eukaryotic translation initiation factor 3 subunit 8 (eif3 p110) (eif3c). [swissprot;acc:q99613] 923 4057.54 1.09861 4457.66
    eukaryotic translation initiation factor 3 subunit 9 (eif-3 eta) (eif3 p116) (eif3 p110) (eif3b). [swissprot;acc:p55884] 684 4359.82 1.11954 4880.99
    eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] 186 4071.1 1.29001 5251.75
    eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] 181 4068.56 1.29102 5252.6
    eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730] 393 4490.28 1.16301 5222.25
    eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] 273 3199.4 1.20985 3870.8
    eukaryotic translation initiation factor 5a (eif-5a) (eif-4d) (rev- binding factor). [swissprot;acc:p10159] 1612 6212.98 1.07116 6655.12
    eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [swissprot;acc:p56537] 506 3893.85 1.14308 4450.98
    evolutionarily conserved g-patch domain containing. [refseq;acc:nm_018025] 1652 5944.24 1.06962 6358.1
    evolutionarily conserved signaling intermediate in toll pathway; ecsit. [refseq;acc:nm_016581] 1537 6184.27 1.07328 6637.44
    exocyst complex component exo70. [swissprot;acc:q9upt5] 2781 0.00001 1 0.00001
    exocyst complex component sec10 (hsec10). [swissprot;acc:o00471] 1438 6721.25 1.07693 7238.34
    exocyst complex component sec15a. [swissprot;acc:q8tag9] 1068 6201.54 1.09237 6774.35
    exocyst complex component sec15b. [swissprot;acc:q9y2d4] 1083 6213.51 1.09198 6785.04
    exocyst complex component sec3 (bm-012). [swissprot;acc:q9nv70] 2048 6036.68 1.05678 6379.44
    exocyst complex component sec5. [swissprot;acc:q96kp1] 286 23316 1.20878 19288.8
    exocyst complex component sec6. [swissprot;acc:o60645] 2135 7387.42 1.05388 7785.45
    exocyst complex component sec8. [swissprot;acc:q96a65] 1311 6221.22 1.08142 6727.77
    exonuclease 1 isoform b; rad2 nuclease family member, homolog of s. cerevisiae exonuclease 1. [refseq;acc:nm_006027] 2170 5825.61 1.05169 6126.74
    exosome complex exonuclease rrp4 (ec 3.1.13.-) (ribosomal rna processing protein 4). [swissprot;acc:q13868] 2594 4921.84 1.01691 5005.06
    exosome complex exonuclease rrp40 (ec 3.1.13.-) (ribosomal rna processing protein 40) (p10) (cgi-102). [swissprot;acc:q9nqt5] 2595
    exosome complex exonuclease rrp41 (ec 3.1.13.-) (ribosomal rna processing protein 41) (p12a). [swissprot;acc:q9npd3] 2593
    exosome complex exonuclease rrp46 (ec 3.1.13.-) (ribosomal rna processing protein 46) (p12b) (chronic myelogenous leukemia tumor antigen 28). [swissprot;acc:q9nqt4] 2596
    exportin 1; exportin-1 (required for chromosome region maintenance); exportin 1 (crm1, yeast, homolog); crm1, yeast, homolog. [refseq;acc:nm_003400] 826 5195.58 1.10678 5750.34
    eyes absent homolog 1. [swissprot;acc:q99502] 2268 5785.08 1.04597 6051.03

    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
    - 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/