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 Filtered Interaction Map red green network_comparison
    Results: HTML CSV LaTeX Showing element 1051 to 1100 of 8289 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Filtered  : 1
    description
    		Rank
    		Interaction Map
    		red
    		green
    		network_comparison
    bone morphogenetic protein 6 precursor (bmp-6). [swissprot;acc:p22004] 2896 High confidence 0.00001 0.00001 1
    2923 Low confidence 203.481 200.077 1.01701
    bone morphogenetic protein 7 precursor (bmp-7) (osteogenic protein 1) (op-1). [swissprot;acc:p18075] 2943 203.455 200.059 1.01697
    3128 High confidence 0.00001 0.00001 1
    bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [swissprot;acc:p34820] 2773
    2910 Low confidence 203.494 200.087 1.01703
    brachyury protein (t protein). [swissprot;acc:o15178] 56 224.922 202.592 1.11022
    2040 High confidence 210.586 208.803 1.00854
    brain link protein-1 precursor. [swissprot;acc:q9gzv7] 2642 Low confidence 203.73 200.174 1.01776
    brain protein 16. [refseq;acc:nm_016458] 1847 High confidence 216.811 219.195 1.011
    2180 Low confidence 188.304 184.788 1.01903
    brain protein 44-like protein (hspc040) (cgi-129) (pnas-115). [swissprot;acc:q9y5u8] 1080 196.378 191.803 1.02385
    brain protein 44. [swissprot;acc:o95563] 742 High confidence 126.215 120.078 1.05111
    1040 Low confidence 182.902 178.58 1.0242
    branched-chain amino acid aminotransferase, cytosolic (ec 2.6.1.42) (bcat(c)) (eca39 protein). [swissprot;acc:p54687] 1867 199.922 196.027 1.01987
    2672 High confidence 210.957 210.741 1.00102
    branched-chain amino acid aminotransferase, mitochondrial precursor (ec 2.6.1.42) (bcat(m)) (placental protein 18) (pp18). [swissprot;acc:o15382] 1877 Low confidence 199.88 195.99 1.01985
    2687 High confidence 210.939 210.755 1.00087
    brca1 associated protein. [refseq;acc:nm_006768] 3161 0.00001 0.00001 1
    4538 Low confidence 177.657 176.223 1.00814
    brca1-associated ring domain protein 1 (bard-1). [swissprot;acc:q99728] 1752 High confidence 216.271 218.991 1.01258
    3479 Low confidence 199.172 196.226 1.01501
    brca2 and cdkn1a-interacting protein isoform bccipalpha; brca2 and cdkn1a-interacting protein; cdk inhibitor p21 binding protein; bccipalpha; bccipbeta; tok-1alpha; tok-1beta. [refseq;acc:nm_016567] 294 High confidence 240.782 265.717 1.10356
    1490 Low confidence 202.583 198.329 1.02145
    breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] 229 High confidence 226.401 202.094 1.12028
    603 Low confidence 201.427 195.587 1.02986
    breast cancer antigen ny-br-1. [refseq;acc:nm_052997] 262 216.842 207.332 1.04587
    breast cancer type 1 susceptibility protein. [swissprot;acc:p38398] 939 High confidence 216.501 224.27 1.03588
    3636 Low confidence 201.391 198.576 1.01418
    breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872] 691 High confidence 217.602 206.195 1.05532
    1733 Low confidence 202.346 198.294 1.02043
    brefeldin a-inhibited guanine nucleotide-exchange protein 1 (brefeldin a-inhibited gep 1) (p200 arf-gep1) (p200 arf guanine nucleotide exchange factor). [swissprot;acc:q9y6d6] 647 203.293 197.621 1.0287
    2713 High confidence 220.521 220.395 1.00057
    brefeldin a-inhibited guanine nucleotide-exchange protein 2 (brefeldin a-inhibited gep 2). [swissprot;acc:q9y6d5] 649 Low confidence 203.283 197.617 1.02867
    2711 High confidence 220.521 220.395 1.00057
    brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732] 597 Low confidence 204.856 198.854 1.03018
    945 High confidence 212.44 205.085 1.03586
    bromodomain adjacent to zinc finger domain protein 1a (atp-utilizing chromatin assembly and remodeling factor 1) (hacf1) (atp-dependent chromatin remodelling protein) (williams syndrome transcription factor-related chromatin remodeling factor 180) (wcrf180) (hwalp1) (chrac subunit acf1) (hspc317). [swissprot;acc:q9nrl2] 183 Low confidence 196.372 206.947 1.05385
    bromodomain and phd finger-containing protein 3 (fragment). [swissprot;acc:q9uld4] 3149 High confidence 0.00001 0.00001 1
    3354 Low confidence 204.204 201.079 1.01554
    bromodomain containing 7; bromodomain protein; bromodomain-containing 7. [refseq;acc:nm_013263] 1002 205.137 200.227 1.02452
    2747 High confidence 201.477 201.514 1.00018
    bromodomain containing 8; thyroid hormone receptor coactivating protein; skeletal muscle abundant protein. [refseq;acc:nm_006696] 573 Low confidence 206.46 200.275 1.03088
    bromodomain-containing protein 1 (br140-like protein). [swissprot;acc:o95696] 3139 High confidence 0.00001 0.00001 1
    3352 Low confidence 204.204 201.079 1.01554
    bromodomain-containing protein 2 (ring3 protein) (o27.1.1). [swissprot;acc:p25440] 2241 High confidence 222.96 224.338 1.00618
    3324 Low confidence 197.238 194.204 1.01562
    bromodomain-containing protein 3 (ring3-like protein). [swissprot;acc:q15059] 2237 High confidence 222.965 224.343 1.00618
    3350 Low confidence 197.071 194.055 1.01554
    bromodomain-containing protein 4 (hunk1 protein). [swissprot;acc:o60885] 2238 High confidence 222.959 224.337 1.00618

    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/