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 green Filtered red network_comparison
    Results: HTML CSV LaTeX Showing element 501 to 550 of 8289 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Filtered  : 1
    description
    		Rank
    		Interaction Map
    		green
    		red
    		network_comparison
    adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] 4467 Low confidence 210.017 208.138 1.00903
    adenylosuccinate lyase (ec 4.3.2.2) (adenylosuccinase) (asl) (asase). [swissprot;acc:p30566] 1608 195.607 199.691 1.02088
    2067 High confidence 191.639 193.226 1.00828
    adenylosuccinate synthase-like 1. [refseq;acc:nm_152328] 1192 Low confidence 194.529 199.02 1.02309
    1661 High confidence 201.551 204.437 1.01432
    adenylosuccinate synthetase (ec 6.3.4.4) (imp--aspartate ligase) (adss) (ampsase). [swissprot;acc:p30520] 1200 Low confidence 194.493 198.973 1.02303
    1665 High confidence 201.564 204.433 1.01423
    adenylyl cyclase-associated protein 1 (cap 1). [swissprot;acc:q01518] 1701 Low confidence 197.403 201.46 1.02055
    1850 High confidence 213.587 215.931 1.01097
    adenylyl cyclase-associated protein 2 (cap 2). [swissprot;acc:p40123] 1699 Low confidence 197.367 201.425 1.02056
    1895 High confidence 213.639 215.853 1.01036
    adhesion regulating molecule 1 precursor (110 kda cell membrane glycoprotein) (gp110). [swissprot;acc:q16186] 2369 219.434 218.555 1.00402
    2525 Low confidence 199.602 203.221 1.01813
    adipocyte plasma membrane-associated protein (bscv protein). [swissprot;acc:q9hdc9] 813 High confidence 221.785 212.386 1.04425
    3843 Low confidence 198.793 201.394 1.01308
    adiponectin receptor 2. [refseq;acc:nm_024551] 104 204.212 219.277 1.07377
    185 High confidence 246.371 281.582 1.14292
    adp,atp carrier protein, fibroblast isoform (adp/atp translocase 2) (adenine nucleotide translocator 2) (ant 2). [swissprot;acc:p05141] 1552 221.424 225.159 1.01687
    1779 Low confidence 195.272 199.221 1.02022
    adp,atp carrier protein, heart/skeletal muscle isoform t1 (adp/atp translocase 1) (adenine nucleotide translocator 1) (ant 1). [swissprot;acc:p12235] 1551 High confidence 221.424 225.159 1.01687
    1772 Low confidence 195.276 199.226 1.02023
    adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236] 1550 High confidence 221.424 225.159 1.01687
    1780 Low confidence 195.256 199.201 1.0202
    adp-ribose pyrophosphatase (ec 3.6.1.13) (adp-ribose diphosphatase) (adenosine diphosphoribose pyrophosphatase) (adpr-ppase) (adp-ribose phosphohydrolase) (nucleoside diphosphate-linked moiety x motif 9). [swissprot;acc:q9bw91] 2492 200.307 203.957 1.01822
    adp-ribosylation factor 1. [swissprot;acc:p32889] 1229 198.315 202.83 1.02277
    2128 High confidence 222.788 221.248 1.00696
    adp-ribosylation factor 3. [swissprot;acc:p16587] 1164 Low confidence 198.252 202.869 1.02329
    2130 High confidence 222.788 221.248 1.00696
    adp-ribosylation factor 4. [swissprot;acc:p18085] 1165 Low confidence 198.216 202.831 1.02328
    2123 High confidence 222.788 221.248 1.00696
    adp-ribosylation factor 5. [swissprot;acc:p26437] 3558 Low confidence 196.554 199.425 1.01461
    adp-ribosylation factor binding protein gga1 (golgi-localized, gamma ear-containing, arf-binding protein 1) (gamma-adaptin related protein 1). [swissprot;acc:q9ujy5] 3022 196.696 199.98 1.0167
    adp-ribosylation factor binding protein gga2 (golgi-localized, gamma ear-containing, arf-binding protein 2) (gamma-adaptin related protein 2) (vear) (vhs domain and ear domain of gamma-adaptin). [swissprot;acc:q9ujy4] 3016 196.697 199.984 1.01671
    adp-ribosylation factor binding protein gga3 (golgi-localized, gamma ear-containing, arf-binding protein 3). [swissprot;acc:q9nz52] 3030 196.693 199.971 1.01667
    adp-ribosylation factor gtpase activating protein 1 (adp-ribosylation factor 1 gtpase activating protein) (arf1 gap) (arf1-directed gtpase- activating protein) (gap protein). [swissprot;acc:q8n6t3] 2156 High confidence 198.71 200.063 1.00681
    2704 Low confidence 195.675 199.109 1.01755
    adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] 2137 High confidence 222.788 221.248 1.00696
    3196 Low confidence 197.655 200.829 1.01606
    adp-ribosylation factor guanine nucleotide factor 6; hepatocellular carcinoma-associated antigen 67. [refseq;acc:nm_015310] 4149 198.625 200.724 1.01057
    adp-ribosylation factor-like protein 1. [swissprot;acc:p40616] 2613 High confidence 215.799 215.497 1.0014
    4075 Low confidence 198.695 200.896 1.01108
    adp-ribosylation factor-like protein 3. [swissprot;acc:p36405] 2520 High confidence 216.341 215.835 1.00234
    4553 Low confidence 200.827 202.436 1.00801
    adp-ribosylation factor-like protein 4. [swissprot;acc:p40617] 1188 High confidence 212.904 218.402 1.02582
    2587 Low confidence 194.454 197.95 1.01798
    adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559] 1186 High confidence 212.904 218.402 1.02582
    2585 Low confidence 194.454 197.95 1.01798
    adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [swissprot;acc:p10109] 1074 187.103 191.57 1.02387
    1105 High confidence 185.882 191.139 1.02828
    adrenoleukodystrophy protein (aldp). [swissprot;acc:p33897] 1553 Low confidence 206.704 202.418 1.02117

    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/