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 green network_comparison
    Results: HTML CSV LaTeX Showing element 101 to 150 of 3228 in total
    Value Type  : Measured
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    description
    		Rank
    		red
    		green
    		network_comparison
    5-aminolevulinic acid synthase, erythroid-specific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-e). [swissprot;acc:p22557] 1910 6858.84 7287.27 1.06246
    5-aminolevulinic acid synthase, nonspecific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-h). [swissprot;acc:p13196] 1915
    5-formyltetrahydrofolate cyclo-ligase (ec 6.3.3.2) (5,10-methenyl- tetrahydrofolate synthetase) (methenyl-thf synthetase) (mthfs). [swissprot;acc:p49914] 1833 6175.23 6572.85 1.06439
    5-methyltetrahydrofolate--homocysteine methyltransferase (ec 2.1.1.13) (methionine synthase, vitamin-b12 dependent) (ms). [swissprot;acc:q99707] 1115 5795.13 6314.19 1.08957
    54 kda nuclear rna- and dna-binding protein (p54(nrb)) (p54nrb) (55 kda nuclear protein) (nmt55) (non-pou domain-containing octamer- binding protein) (dna-binding p52/p100 complex, 52 kda subunit). [swissprot;acc:q15233] 2028 10243.4 9686.82 1.05746
    6-phosphofructokinase, liver type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme b) (pfk-b). [swissprot;acc:p17858] 764 4250.18 4729.12 1.11269
    6-phosphofructokinase, muscle type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme a) (pfk-a) (phosphofructokinase-m). [swissprot;acc:p08237] 763 4250.54 4729.67 1.11272
    6-phosphofructokinase, type c (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme c) (pfk-c) (6-phosphofructokinase, platelet type). [swissprot;acc:q01813] 759 4254.62 4736.03 1.11315
    6-phosphogluconate dehydrogenase, decarboxylating (ec 1.1.1.44). [swissprot;acc:p52209] 1339 5988.06 6464.94 1.07964
    6-phosphogluconolactonase (ec 3.1.1.31) (6pgl). [swissprot;acc:o95336] 1627 6038.46 6463.9 1.07046
    6-pyruvoyl tetrahydrobiopterin synthase (ec 4.2.3.12) (ptps) (ptp synthase). [swissprot;acc:q03393] 2904 0.00001 0.00001 1
    60 kda heat shock protein, mitochondrial precursor (hsp60) (60 kda chaperonin) (cpn60) (heat shock protein 60) (hsp-60) (mitochondrial matrix protein p1) (p60 lymphocyte protein) (hucha60). [swissprot;acc:p10809] 1313 5457.14 5899.85 1.08112
    60 kda tat interactive protein (tip60) (hiv-1 tat interactive protein) (cpla(2) interacting protein). [swissprot;acc:q92993] 1751 6011.57 6414.98 1.06711
    60s acidic ribosomal protein p0 (l10e). [swissprot;acc:p05388] 2258 5150.31 5388.05 1.04616
    60s acidic ribosomal protein p1. [swissprot;acc:p05386] 2418 4857.03 5039.78 1.03763
    60s acidic ribosomal protein p2. [swissprot;acc:p05387] 2743 4824.49 4813.92 1.0022
    60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] 2233 3614.08 3450.07 1.04754
    60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025] 2255 3624.59 3463.37 1.04655
    60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [swissprot;acc:q9y3b7] 2417 3598.55 3467.65 1.03775
    60s ribosomal protein l11. [swissprot;acc:p39026] 1834 3593.24 3375.93 1.06437
    60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] 2186 3586.3 3414.4 1.05035
    60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815] 2372 3677.53 3526.65 1.04278
    60s ribosomal protein l12. [swissprot;acc:p30050] 2185 3586.32 3414.42 1.05035
    60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1] 2447 3730.53 3611.05 1.03309
    60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429] 2449 3730.74 3611.45 1.03303
    60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914] 2074 3614.91 3423.89 1.05579
    60s ribosomal protein l15. [swissprot;acc:p39030] 2532 4888.72 5006.1 1.02401
    60s ribosomal protein l17 (l23). [swissprot;acc:p18621] 1894 3598.08 3384.59 1.06308
    60s ribosomal protein l18. [swissprot;acc:q07020] 2694 4113.79 4095.53 1.00446
    60s ribosomal protein l18a. [swissprot;acc:q02543] 806 4708.61 5226.71 1.11003
    60s ribosomal protein l19. [swissprot;acc:p14118] 2136 3687.49 3499.2 1.05381
    60s ribosomal protein l21. [swissprot;acc:p46778] 1510 5546.11 5957.99 1.07426
    60s ribosomal protein l22 (epstein-barr virus small rna associated protein) (eber associated protein) (eap) (heparin binding protein hbp15). [swissprot;acc:p35268] 2673 7780.98 7741.14 1.00515
    60s ribosomal protein l23 (l17). [swissprot;acc:p23131] 2115 3672.49 3482.34 1.0546
    60s ribosomal protein l23a. [swissprot;acc:p29316] 2175 3642.13 3463.88 1.05146
    60s ribosomal protein l24 (l30). [swissprot;acc:p38663] 727 7087.23 7911.25 1.11627
    60s ribosomal protein l26. [swissprot;acc:q02877] 2051 3601.97 3409.48 1.05646
    60s ribosomal protein l28. [swissprot;acc:p46779] 1548 5987.29 6423.52 1.07286
    60s ribosomal protein l29 (cell surface heparin binding protein hip). [swissprot;acc:p47914] 1648 6079.19 6503.12 1.06973
    60s ribosomal protein l3-like. [swissprot;acc:q92901] 2114 3617.81 3430.31 1.05466
    60s ribosomal protein l30. [swissprot;acc:p04645] 2386 3674.02 3529.35 1.04099
    60s ribosomal protein l31. [swissprot;acc:p12947] 808 4708.61 5226.71 1.11003
    60s ribosomal protein l32. [swissprot;acc:p02433] 1798 3618.02 3394.29 1.06591
    60s ribosomal protein l34, mitochondrial precursor (l34mt). [swissprot;acc:q9bq48] 1300 5589.33 6047.9 1.08204
    60s ribosomal protein l34. [swissprot;acc:p49207] 2077 3614.91 3423.89 1.05579
    60s ribosomal protein l35. [swissprot;acc:p42766] 2065 3602.25 3410.23 1.05631
    60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6] 2264 3633.74 3473.68 1.04608
    60s ribosomal protein l37 (g1.16). [swissprot;acc:p02403] 2548 4725.79 4824.4 1.02087
    60s ribosomal protein l37a. [swissprot;acc:p12751] 2959 0.00001 0.00001 1
    60s ribosomal protein l39. [swissprot;acc:p02404] 805 4708.61 5226.71 1.11003

    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/