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.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


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description Rank Gene Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1068 to 1117 of 3228 in total
Value Type  : Measured
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
description
Rank
red
green
network_comparison
fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263] 733 13241.4 11864 1.1161
g protein-coupled receptor 66. [refseq;acc:nm_006056] 2815 0.00001 0.00001 1
g-rich sequence factor-1 (grsf-1). [swissprot;acc:q12849] 1396 5803.54 6256.54 1.07806
g1 to s phase transition protein 1 homolog (gtp-binding protein gst1-hs). [swissprot;acc:p15170] 1336 6140.18 6632.24 1.08014
g2/mitotic-specific cyclin b1. [swissprot;acc:p14635] 362 12786.6 10879.9 1.17525
g2/mitotic-specific cyclin b2. [swissprot;acc:o95067] 360 12796.8 10886 1.17553
ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [swissprot;acc:q06546] 455 4890.51 5610.95 1.14731
ga binding protein beta-2 chain (gabp-beta-2 subunit) (transcription factor e4tf1-47) (gapbp-2) (nuclear respiratory factor-2 subunit gamma). [swissprot;acc:q06545] 456
gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] 133 23421.5 17580.4 1.33225
gaba-a receptor-associated protein. [sptrembl;acc:q9by60] 134 21785.2 16426.1 1.32626
galactose-1-phosphate uridylyltransferase (ec 2.7.7.12) (gal-1-p uridylyltransferase) (udp-glucose--hexose-1-phosphate uridylyltransferase). [swissprot;acc:p07902] 517 4910.6 5600.61 1.14051
galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470] 966 7817.9 8575.12 1.09686
galectin-9 (hom-hd-21) (ecalectin). [swissprot;acc:o00182] 973 7810.11 8566.29 1.09682
gamma adducin (adducin-like protein 70). [swissprot;acc:q9uey8] 1365 5799.14 6255.04 1.07862
gamma enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (neural enolase) (nse) (enolase 2). [swissprot;acc:p09104] 943 6597.98 7241 1.09746
gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [swissprot;acc:p14867] 587 6739.83 7644.63 1.13425
gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p47869] 580
gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [swissprot;acc:p34903] 588
gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [swissprot;acc:p48169] 584 6739.82
gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [swissprot;acc:q16445] 581
gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334] 585
gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [swissprot;acc:q8n1c3] 579 7644.62
gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p18507] 582
gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [swissprot;acc:q99928] 577 6739.81
gamma-butyrobetaine,2-oxoglutarate dioxygenase (ec 1.14.11.1) (gamma-butyrobetaine hydroxylase) (gamma-bbh). [swissprot;acc:o75936] 1348 6153.36 6640.77 1.07921
gamma-interferon inducible lysosomal thiol reductase precursor (gamma-interferon-inducible protein ip-30). [swissprot;acc:p13284] 3101 0.00001 0.00001 1
gamma-sarcoglycan (gamma-sg) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q13326] 741 5768.32 6434.78 1.11554
gamma-snap-associated factor 1; rab11-interacting protein. [refseq;acc:nm_015470] 1450 5602.01 6031.05 1.07659
gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747] 500 4682.87 4093.05 1.1441
ganglioside-induced differentiation-associated protein 1-like 1. [refseq;acc:nm_024034] 776 5874.76 6533.36 1.11211
ganglioside-induced differentiation-associated protein 1. [refseq;acc:nm_018972] 779
gastricsin precursor (ec 3.4.23.3) (pepsinogen c). [swissprot;acc:p20142] 1188 4392.63 4776.19 1.08732
gbp protein isoform a. [refseq;acc:nm_017870] 23 699.76 1894.39 2.7072
gc-rich sequence dna-binding factor homolog. [swissprot;acc:q9y5b6] 1685 6088.07 6508.45 1.06905
gcn5-like protein 1 (rt14 protein). [swissprot;acc:p78537] 2432 8154.48 8453.84 1.03671
gdp-fucose protein o-fucosyltransferase 1 precursor (ec 2.4.1.221) (peptide o-fucosyltransferase) (o-fuct-1). [swissprot;acc:q9h488] 3125 0.00001 0.00001 1
gdp-mannose pyrophosphorylase a; mannose-1-phosphate guanylyltransferase (gdp). [refseq;acc:nm_013335] 1520 5283.8 5673.81 1.07381
gdp-mannose pyrophosphorylase b isoform 1; mannose-1-phosphate guanylyltransferase; amphoterin induced gene 3. [refseq;acc:nm_013334] 1519
general control of amino acid synthesis protein 5-like 2 (ec 2.3.1.-) (histone acetyltransferase gcn5) (hsgcn5). [swissprot;acc:q92830] 1944 7210.64 7648.94 1.06079
general vesicular transport factor p115 (transcytosis associated protein) (tap) (vesicle docking protein). [swissprot;acc:o60763] 2156 5701.81 6000.03 1.0523
geranylgeranyl pyrophosphate synthetase (ggpp synthetase) (ggppsase) (geranylgeranyl diphosphate synthase) [includes: dimethylallyltransferase (ec 2.5.1.1); geranyltranstransferase (ec 2.5.1.10); farnesyltranstransferase (ec 2.5.1.29)]. [swissprot;acc:o95749] 1203 4322.65 4696.04 1.08638
geranylgeranyl transferase type i beta subunit (ec 2.5.1.-) (type i protein geranyl-geranyltransferase beta subunit) (ggtase-i-beta). [swissprot;acc:p53609] 2366 5265.95 5492.28 1.04298
geranylgeranyl transferase type ii beta subunit (ec 2.5.1.-) (rab geranylgeranyltransferase beta subunit) (rab geranyl- geranyltransferase beta subunit) (rab gg transferase beta) (rab ggtase beta). [swissprot;acc:p53611] 2963 0.00001 0.00001 1
germ cell specific y-box binding protein; contrin. [refseq;acc:nm_015982] 2096 6682.05 7051.02 1.05522
germ cell-less. [refseq;acc:nm_022471] 2465 7764.92 8003.67 1.03075
gk001 protein. [refseq;acc:nm_020198] 540 10603.5 12069.4 1.13825
glia maturation factor gamma (gmf-gamma). [swissprot;acc:o60234] 1205 5946.33 6459.79 1.08635
glioma pathogenesis-related protein (glipr) (rtvp-1 protein). [swissprot;acc:p48060] 2953 0.00001 0.00001 1
glioma tumor suppressor candidate region gene 2 protein (p60). [swissprot;acc:q9nzm5] 3104
glioma-amplified sequence-41; numa binding protein 1. [refseq;acc:nm_006530] 3007

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/