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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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 3013 to 3062 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1507 atp synthase coupling factor b, mitochondrial precursor. [swissprot;acc:q99766] Divided 6152.78 6610.46 1.07439
phosphoinositide-3-kinase, class 2, alpha polypeptide; c2-containing phosphatidylinositol kinase. [refseq;acc:nm_002645] Subtracted 6326.24 6762.27 436.03
1508 f-actin capping protein alpha-3 subunit (capz alpha-3) (germ cell- specific protein 3). [swissprot;acc:q96kx2] 6304.74 6740.66 435.92
guanine deaminase (ec 3.5.4.3) (guanase) (guanine aminase) (guanine aminohydrolase) (gah) (p51-nedasin). [swissprot;acc:q9y2t3] Divided 6152.78 6610.46 1.07439
1509 acetyl-coa carboxylase 2 (ec 6.4.1.2) (acc-beta) [includes: biotin carboxylase (ec 6.3.4.14)]. [swissprot;acc:o00763] 7237.39 7775.21 1.07431
f-actin capping protein beta subunit (capz beta). [swissprot;acc:p47756] Subtracted 6304.74 6740.66 435.92
1510 60s ribosomal protein l21. [swissprot;acc:p46778] Divided 5546.11 5957.99 1.07426
phospholipase d1 (ec 3.1.4.4) (pld 1) (choline phosphatase 1) (phosphatidylcholine-hydrolyzing phospholipase d1) (hpld1). [swissprot;acc:q13393] Subtracted 6153.79 6589.52 435.73
1511 26s protease regulatory subunit 6a (tat-binding protein 1) (tbp-1) (proteasome subunit p50). [swissprot;acc:p17980] 5926.76 6362.33 435.57
serine/threonine protein phosphatase 6 (ec 3.1.3.16) (pp6). [swissprot;acc:o00743] Divided 7234.61 7771.58 1.07422
1512 importin 7; ran-binding protein 7. [refseq;acc:nm_006391] Subtracted 5628.53 6063.61 435.08
sporulation-induced transcript 4-associated protein. [refseq;acc:nm_018312] Divided 7234.61 7771.58 1.07422
1513 importin 8; ran-binding protein 8. [refseq;acc:nm_006390] Subtracted 5628.53 6063.61 435.08
proteasome subunit beta type 10 precursor (ec 3.4.25.1) (proteasome mecl-1) (macropain subunit mecl-1) (multicatalytic endopeptidase complex subunit mecl-1). [swissprot;acc:p40306] Divided 6079.65 6530.82 1.07421
1514 acetyl-coa carboxylase 1 (ec 6.4.1.2) (acc-alpha) [includes: biotin carboxylase (ec 6.3.4.14)]. [swissprot;acc:q13085] 7232.14 7768.35 1.07414
brefeldin a-inhibited guanine nucleotide-exchange protein 2 (brefeldin a-inhibited gep 2). [swissprot;acc:q9y6d5] Subtracted 5628.53 6063.61 435.08
1515 hsgcn1 (fragment). [sptrembl;acc:q99736]
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] Divided 5633.67 6050.69 1.07402
1516 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] Subtracted 5628.53 6063.61 435.08
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] Divided 5633.67 6050.69 1.07402
1517 26s proteasome non-atpase regulatory subunit 9 (26s proteasome regulatory subunit p27). [swissprot;acc:o00233] 5996.14 6439.46 1.07393
camp response element-binding protein cre-bpa. [refseq;acc:nm_004904] Subtracted 5658.8 6093.56 434.76
1518 anaphase-promoting complex subunit 2; anaphase-promoting complex 2. [refseq;acc:nm_013366] Divided 10341.2 9630.35 1.07381
hepatocyte nuclear factor 3-alpha (hnf-3a) (forkhead box protein a1). [swissprot;acc:p55317] Subtracted 5787.03 6221.72 434.69
1519 gdp-mannose pyrophosphorylase b isoform 1; mannose-1-phosphate guanylyltransferase; amphoterin induced gene 3. [refseq;acc:nm_013334] Divided 5283.8 5673.81 1.07381
wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [swissprot;acc:q9upy6] Subtracted 6304.21 6738.77 434.56
1520 gdp-mannose pyrophosphorylase a; mannose-1-phosphate guanylyltransferase (gdp). [refseq;acc:nm_013335] Divided 5283.8 5673.81 1.07381
rest corepressor. [refseq;acc:nm_015156] Subtracted 6304.21 6738.77 434.56
1521 26s protease regulatory subunit 4 (p26s4). [swissprot;acc:q03527] Divided 5938.56 6376.76 1.07379
wiskott-aldrich syndrome protein family member 2 (wasp-family protein member 2) (verprolin homology domain-containing protein 2). [swissprot;acc:q9y6w5] Subtracted 6304.22 6738.77 434.55
1522 glycerol kinase, testis specific 1 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14409] Divided 6137.24 6589.72 1.07373
wiskott-aldrich syndrome protein family member 1 (wasp-family protein member 1) (verprolin homology domain-containing protein 1). [swissprot;acc:q92558] Subtracted 6304.22 6738.77 434.55
1523 glycerol kinase (ec 2.7.1.30) (atp:glycerol 3-phosphotransferase) (glycerokinase) (gk). [swissprot;acc:p32189] Divided 6137.09 6589.57 1.07373
structure-specific recognition protein 1 (ssrp1) (recombination signal sequence recognition protein) (t160) (chromatin-specific transcription elongation factor 80 kda subunit) (fact 80 kda subunit). [swissprot;acc:q08945] Subtracted 4483.26 4917.77 434.51
1524 chromatin-specific transcription elongation factor large subunit. [refseq;acc:nm_007192]
glycerol kinase, testis specific 2 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14410] Divided 6137.53 6590.01 1.07372
1525 dna fragmentation factor 40 kda subunit (ec 3.-.-.-) (dff-40) (caspase-activated deoxyribonuclease) (caspase-activated dnase) (cad) (caspase-activated nuclease) (cpan). [swissprot;acc:o76075] Subtracted 5916.05 6350.53 434.48
tensin. [refseq;acc:nm_022648] Divided 5871.89 6303.56 1.07351
1526 adamts-9 precursor (ec 3.4.24.-) (a disintegrin and metalloproteinase with thrombospondin motifs 9) (adam-ts 9) (adam-ts9). [swissprot;acc:q9p2n4] Subtracted 5916.05 6350.53 434.48
calreticulin precursor (crp55) (calregulin) (hacbp) (erp60). [swissprot;acc:p27797] Divided 5369.1 5763.72 1.0735
1527 26s protease regulatory subunit 6a (tat-binding protein 1) (tbp-1) (proteasome subunit p50). [swissprot;acc:p17980] 5926.76 6362.33 1.07349
dna fragmentation factor alpha subunit (dna fragmentation factor 45 kda subunit) (dff-45) (inhibitor of cad) (icad). [swissprot;acc:o00273] Subtracted 5916.05 6350.53 434.48
1528 ankyrin 3 (ank-3) (ankyrin g). [swissprot;acc:q12955]
c1 domain-containing phosphatase and tensin-like protein isoform 2; putative protein tyrosine phosphatase; c1 domain-containing phosphatase and tensin-like protein; tensin 2. [refseq;acc:nm_015319] Divided 5869.97 6301.24 1.07347
1529 ankyrin 2 (brain ankyrin) (ankyrin b) (ankyrin, nonerythroid). [swissprot;acc:q01484] Subtracted 5916.05 6350.53 434.48
dna fragmentation factor 40 kda subunit (ec 3.-.-.-) (dff-40) (caspase-activated deoxyribonuclease) (caspase-activated dnase) (cad) (caspase-activated nuclease) (cpan). [swissprot;acc:o76075] Divided 1.07344
1530 adamts-9 precursor (ec 3.4.24.-) (a disintegrin and metalloproteinase with thrombospondin motifs 9) (adam-ts 9) (adam-ts9). [swissprot;acc:q9p2n4]
adp-ribosylation factor-like protein 3. [swissprot;acc:p36405] Subtracted 434.48
1531 dna fragmentation factor alpha subunit (dna fragmentation factor 45 kda subunit) (dff-45) (inhibitor of cad) (icad). [swissprot;acc:o00273] Divided 1.07344
unc-119 protein homolog (retinal protein 4) (hrg4). [swissprot;acc:q13432] Subtracted 434.48

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/