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 [...,...].
    Filtered green Value Type Network Comparison Type Gene red Interaction Map network_comparison Rank description
    Results: HTML CSV LaTeX Showing element 501 to 550 of 77072 in total
    Filtered  : 0
    green
    Value Type
    Network Comparison Type
    red
    Interaction Map
    network_comparison
    Rank
    description
    5.39669 Squared Divided 1.22698 High confidence 4.39835 52 selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611]
    Low confidence 56
    33.64 High confidence 6.23345 42 nanos (fragment). [sptrembl;acc:q8wy41]
    Subtracted 1.22698 4.16971 420 selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611]
    Low confidence 774
    33.64 High confidence 28.2433 358 nanos (fragment). [sptrembl;acc:q8wy41]
    5.42219 Divided 12.5892 2.32179 91 lats homolog 1. [refseq;acc:nm_004690]
    92 sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5]
    Low confidence 90 lats homolog 1. [refseq;acc:nm_004690]
    91 sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5]
    Subtracted High confidence 7.16701 400 lats homolog 1. [refseq;acc:nm_004690]
    401 sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5]
    Low confidence 761 lats homolog 1. [refseq;acc:nm_004690]
    762 sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5]
    5.56738 Measured Divided 199.549 High confidence 35.8425 11 serpin b12. [swissprot;acc:q96p63]
    Low confidence 10
    Subtracted High confidence 193.982 168
    Low confidence 280
    5.56776 Rooted Divided 5.83095 1.04727 544 adapter-related protein complex 2 alpha 1 subunit (alpha-adaptin a) (adaptor protein complex ap-2 alpha-1 subunit) (clathrin assembly protein complex 2 alpha-a large chain) (100 kda coated vesicle protein a) (plasma membrane adaptor ha2/ap2 adaptin alpha a subunit). [swissprot;acc:o95782]
    Subtracted 0.26319 768
    5.58446 Squared Divided 23.0581 4.12898 61 laminin beta-1 chain precursor (laminin b1 chain). [swissprot;acc:p07942]
    Subtracted 17.4736 732
    5.66499 Rooted Divided 9.92134 High confidence 1.75134 43 40s ribosomal protein s26. [swissprot;acc:p02383]
    Subtracted 4.25635 115
    5.71669 Measured Divided 199.249 34.8539 12 hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]
    Low confidence 11
    Subtracted High confidence 193.532 169
    Low confidence 281
    5.76 Squared Divided 0.0236686 High confidence 243.36 21 succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [swissprot;acc:o14521]
    Subtracted 5.73633 407
    5.80317 Divided 0.0279126 Low confidence 207.905 15 fk506-binding protein 6 (ec 5.2.1.8) (peptidyl-prolyl cis-trans isomerase) (ppiase) (rotamase) (36 kda fk506 binding protein) (fkbp- 36) (immunophilin fkbp36). [swissprot;acc:o75344]
    Subtracted 5.77526 766
    5.80678 Rooted Divided 9.84765 1.69589 32 melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]
    33 melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]
    34 melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]
    35 melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]
    36 hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]
    37 melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]
    39 melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]
    40 melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]
    41 melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]
    42 melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]
    43 melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]
    44 melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]
    45 melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]
    47 melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]
    48 melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1]
    Subtracted 4.04087 196 melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]
    197 melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]
    198 melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]

    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/