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.


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 [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 3251 to 3300 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1626 phospholipase d2 (ec 3.1.4.4) (pld 2) (choline phosphatase 2) (phosphatidylcholine-hydrolyzing phospholipase d2) (pld1c) (hpld2). [swissprot;acc:o14939] Divided 6157.13 6591.53 1.07055
ribonuclease hi large subunit (ec 3.1.26.-) (rnase hi large subunit) (rnase h(35)) (ribonuclease h2) (rnase h2). [swissprot;acc:o75792] Subtracted 6075.19 6496.61 421.42
1627 6-phosphogluconolactonase (ec 3.1.1.31) (6pgl). [swissprot;acc:o95336] Divided 6038.46 6463.9 1.07046
probable ribosome biogenesis protein nep1 (c2f protein). [swissprot;acc:q92979] Subtracted 4076.72 4497.74 421.02
1628 26s protease regulatory subunit 6b (mip224) (mb67 interacting protein) (tat-binding protein-7) (tbp-7). [swissprot;acc:p43686] 5822.25 6242.94 420.69
glycine cleavage system h protein, mitochondrial precursor. [swissprot;acc:p23434] Divided 5920.55 6337.28 1.07039
1629 dimeric dihydrodiol dehydrogenase; 3-deoxyglucosone reductase. [refseq;acc:nm_014475] 6158.32 6590.99 1.07026
gc-rich sequence dna-binding factor homolog. [swissprot;acc:q9y5b6] Subtracted 6088.07 6508.45 420.38
1630 c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545] Divided 9903.22 9253.79 1.07018
toll-like receptor 2 precursor (toll/interleukin 1 receptor-like protein 4). [swissprot;acc:o60603] Subtracted 6088.07 6508.45 420.38
1631 brachyury protein (t protein). [swissprot;acc:o15178] Divided 6179.59 6613.15 1.07016
traf and tnf receptor-associated protein; ets1-associated protein 2. [refseq;acc:nm_016614] Subtracted 5819.37 6239.55 420.18
1632 26s proteasome non-atpase regulatory subunit 13 (26s proteasome regulatory subunit s11) (26s proteasome regulatory subunit p40.5). [swissprot;acc:q9unm6] 5858.48 6278.32 419.84
t-box transcription factor tbx19 (t-box protein 19). [swissprot;acc:o60806] Divided 6179.59 6613.15 1.07016
1633 26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232] Subtracted 5842.44 6261.87 419.43
b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [refseq;acc:nm_181844] Divided 9899.79 9251.2 1.07011
1634 26s proteasome non-atpase regulatory subunit 11 (26s proteasome regulatory subunit s9) (26s proteasome regulatory subunit p44.5). [swissprot;acc:o00231] Subtracted 5853.1 6271.79 418.69
pas domain containing serine/threonine kinase; pas-serine/threonine kinase. [refseq;acc:nm_015148] Divided 9899.73 9251.16 1.07011
1635 b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [swissprot;acc:p41182]
endothelial-derived gene 1. [refseq;acc:nm_025205] Subtracted 6399.54 6818.17 418.63
1636 cop9 complex subunit 4; likely ortholog of mouse cop9 (constitutive photomorphogenic), subunit 4 (arabidopsis); cop9 (constitutive photomorphogenic, arabidopsis, homolog) subunit 4. [refseq;acc:nm_016129] 6988.29 7406.53 418.24
zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623] Divided 9899.73 9251.16 1.07011
1637 ketohexokinase (ec 2.7.1.3) (hepatic fructokinase). [swissprot;acc:p50053] Subtracted 5450.9 5869.07 418.17
proteasome subunit alpha type 6 (ec 3.4.25.1) (proteasome iota chain) (macropain iota chain) (multicatalytic endopeptidase complex iota chain) (27 kda prosomal protein) (pros-27) (p27k). [swissprot;acc:p34062] Divided 6112.4 6540.73 1.07008
1638 c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363] 9895.77 9248.18 1.07002
purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491] Subtracted 5450.9 5869.07 418.17
1639 nicotinamide nucleotide adenylyltransferase 3; pyridine nucleotide adenylyltransferase 3. [refseq;acc:nm_178177] 5573.64 5991.58 417.94
putative inorganic polyphosphate/atp-nad kinase (ec 2.7.1.23) (poly(p)/atp nad kinase). [swissprot;acc:o95544] Divided 5939.71 6354.79 1.06988
1640 adenylosuccinate lyase (ec 4.3.2.2) (adenylosuccinase) (asl) (asase). [swissprot;acc:p30566] 7444.28 7964 1.06981
delta 1-pyrroline-5-carboxylate synthetase (p5cs) [includes: glutamate 5-kinase (ec 2.7.2.11) (gamma-glutamyl kinase) (gk); gamma-glutamyl phosphate reductase (gpr) (ec 1.2.1.41) (glutamate-5-semialdehyde dehydrogenase) (glutamyl-gamma-semialdehyde dehydrogenase)]. [swissprot;acc:p54886] Subtracted 5573.64 5991.58 417.94
1641 ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9] Divided 5782.92 6186.39 1.06977
cleavage and polyadenylation specific factor 6, 68 kd subunit; pre-mrna cleavage factor im (68kd); cleavage and polyadenylation specific factor 6, 68kd subunit; pre-mrna cleavage factor i, 68kd subunit. [refseq;acc:nm_007007] Subtracted 5732.83 6149.86 417.03
1642 40s ribosomal protein s7 (s8). [swissprot;acc:p23821] Divided 5782.92 6186.39 1.06977
lanc lantibiotic synthetase component c-like 2; testis-specific adriamycin sensitivity protein; lanc (bacterial lantibiotic synthetase component c)-like 2; g protein-coupled receptor 69b. [refseq;acc:nm_018697] Subtracted 5633.67 6050.69 417.02
1643 26s proteasome-associated pad1 homolog. [refseq;acc:nm_005805] Divided 5782.92 6186.39 1.06977
lanthionine synthetase c-like protein 1; g protein-coupled receptor 69a; lanc (bacterial lantibiotic synthetase component c)-like 1; lanc (bacterial lantibiotic synthetase component). [refseq;acc:nm_006055] Subtracted 5633.67 6050.69 417.02
1644 apolipoprotein b-100 precursor (apo b-100) [contains: apolipoprotein b-48 (apo b-48)]. [swissprot;acc:p04114] Divided 5782.92 6186.39 1.06977
glycine cleavage system h protein, mitochondrial precursor. [swissprot;acc:p23434] Subtracted 5920.55 6337.28 416.73
1645 bystin. [swissprot;acc:q13895] 4280.99 4697.02 416.03
proto-oncogene tyrosine-protein kinase fes/fps (ec 2.7.1.112) (c-fes). [swissprot;acc:p07332] Divided 6079.19 6503.12 1.06973
1646 26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832] Subtracted 5826.74 6242.44 415.7
molybdenum cofactor synthesis protein 2 large subunit (molybdopterin synthase large subunit) (mpt synthase large subunit) (mocs2b) (moco1- b). [swissprot;acc:o96007] Divided 6079.19 6503.12 1.06973
1647 anaphase-promoting complex subunit 10; anaphase-promoting complex 10. [refseq;acc:nm_014885]
inositol-1(or 4)-monophosphatase 2 (ec 3.1.3.25) (impase 2) (imp 2) (inositol monophosphatase 2) (myo-inositol monophosphatase a2). [swissprot;acc:o14732] Subtracted 6070.41 6485.85 415.44
1648 60s ribosomal protein l29 (cell surface heparin binding protein hip). [swissprot;acc:p47914] Divided 6079.19 6503.12 1.06973
inositol-1(or 4)-monophosphatase (ec 3.1.3.25) (impase) (imp) (inositol monophosphatase) (lithium-sensitive myo-inositol monophosphatase a1). [swissprot;acc:p29218] Subtracted 6069.65 6484.94 415.29
1649 glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 2 (ec 2.6.1.16) (hexosephosphate aminotransferase 2) (d-fructose-6- phosphate amidotransferase 2) (gfat 2) (gfat2). [swissprot;acc:o94808] 5358.19 5773.37 415.18
proto-oncogene tyrosine-protein kinase fer (ec 2.7.1.112) (p94-fer) (c-fer). [swissprot;acc:p16591] Divided 6079.19 6503.12 1.06973
1650 molybdenum cofactor synthesis protein 3 (molybdopterin synthase sulfurylase) (mpt synthase sulfurylase). [swissprot;acc:o95396]
putative inorganic polyphosphate/atp-nad kinase (ec 2.7.1.23) (poly(p)/atp nad kinase). [swissprot;acc:o95544] Subtracted 5939.71 6354.79 415.08

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/