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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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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 2830 to 2879 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1415 caspase-7 precursor (ec 3.4.22.-) (ice-like apoptotic protease 3) (ice-lap3) (apoptotic protease mch-3) (cmh-1). [swissprot;acc:p55210] Subtracted 4633.48 5084.24 450.76
1416 apopain precursor (ec 3.4.22.-) (cysteine protease cpp32) (yama protein) (cpp-32) (caspase-3) (casp-3) (srebp cleavage activity 1) (sca-1). [swissprot;acc:p42574]
xpmc2 prevents mitotic catastrophe 2 homolog; xenopus prevents mitotic catastrophe 2 homolog. [refseq;acc:nm_020385] Divided 6123.75 6597.71 1.0774
1417 isocitrate dehydrogenase [nad] subunit alpha, mitochondrial precursor (ec 1.1.1.41) (isocitric dehydrogenase) (nad+-specific icdh). [swissprot;acc:p50213] 5360.39 5775.24 1.07739
p53-related protein kinase (ec 2.7.1.-) (nori-2). [swissprot;acc:q96s44] Subtracted 5346.11 5796.72 450.61
1418 14-3-3 protein zeta/delta (protein kinase c inhibitor protein-1) (kcip-1) (factor activating exoenzyme s) (fas). [swissprot;acc:p29312] 5815.33 6265.44 450.11
isocitrate dehydrogenase [nad] subunit beta, mitochondrial precursor (ec 1.1.1.41) (isocitric dehydrogenase) (nad+-specific icdh). [swissprot;acc:o43837] Divided 5360.39 5775.24 1.07739
1419 histone deacetylase 9 (hd9) (hd7b) (hd7). [swissprot;acc:q9ukv0] Subtracted 5813.88 6263.97 450.09
isocitrate dehydrogenase [nad] subunit gamma, mitochondrial precursor (ec 1.1.1.41) (isocitric dehydrogenase) (nad+-specific icdh). [swissprot;acc:p51553] Divided 5360.39 5775.24 1.07739
1420 histone deacetylase 5 (hd5) (antigen ny-co-9). [swissprot;acc:q9uql6] Subtracted 5813.84 6263.92 450.08
zinc finger protein zic 1 (zinc finger protein of the cerebellum 1). [swissprot;acc:q15915] Divided 5658.51 6096.21 1.07735
1421 histone deacetylase 4 (hd4). [swissprot;acc:p56524] Subtracted 5813.88 6263.96 450.08
importin 7; ran-binding protein 7. [refseq;acc:nm_006391] Divided 5628.53 6063.61 1.0773
1422 14-3-3 protein beta/alpha (protein kinase c inhibitor protein-1) (kcip-1) (protein 1054). [swissprot;acc:p31946] Subtracted 5812.02 6262.07 450.05
importin 8; ran-binding protein 8. [refseq;acc:nm_006390] Divided 5628.53 6063.61 1.0773
1423 brefeldin a-inhibited guanine nucleotide-exchange protein 2 (brefeldin a-inhibited gep 2). [swissprot;acc:q9y6d5]
lin-7 homolog a; vertebrate lin7 homolog 1; tax interaction protein 33; mammalian lin-7 1. [refseq;acc:nm_004664] Subtracted 5743.45 6193.45 450
1424 hsgcn1 (fragment). [sptrembl;acc:q99736] Divided 5628.53 6063.61 1.0773
lin-7 homolog b; lin-7b protein; likely ortholog of mouse lin-7b; mammalian lin-7 protein 2; likely orholog of mouse lin 7 homolog b (c. elegans). [refseq;acc:nm_022165] Subtracted 5743.39 6192.94 449.55
1425 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] Divided 5628.53 6063.61 1.0773
receptor protein-tyrosine kinase erbb-4 precursor (ec 2.7.1.112) (p180erbb4) (tyrosine kinase-type cell surface receptor her4). [swissprot;acc:q15303] Subtracted 5743.36 6192.72 449.36
1426 2-hydroxyphytanoyl-coa lyase (ec 4.1.-.-) (2-hpcl) (hspc279). [swissprot;acc:q9uj83]
glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 1 (ec 2.6.1.16) (hexosephosphate aminotransferase 1) (d-fructose-6- phosphate amidotransferase 1) (gfat 1) (gfat1). [swissprot;acc:q06210] Divided 5362.85 5777.33 1.07729
1427 receptor protein-tyrosine kinase erbb-3 precursor (ec 2.7.1.112) (c-erbb3) (tyrosine kinase-type cell surface receptor her3). [swissprot;acc:p21860] Subtracted 5743.36 6192.72 449.36
zinc finger protein zic 3 (zinc finger protein of the cerebellum 3). [swissprot;acc:o60481] Divided 5658.55 6095.85 1.07728
1428 dual specificity mitogen-activated protein kinase kinase 1 (ec 2.7.1.-) (map kinase kinase 1) (mapkk 1) (erk activator kinase 1) (mapk/erk kinase 1) (mek1). [swissprot;acc:q02750] 5880.37 6334.71 1.07726
epidermal growth factor receptor precursor (ec 2.7.1.112) (receptor protein-tyrosine kinase erbb-1). [swissprot;acc:p00533] Subtracted 5743.36 6192.7 449.34
1429 receptor protein-tyrosine kinase erbb-2 precursor (ec 2.7.1.112) (p185erbb2) (neu proto-oncogene) (c-erbb-2) (tyrosine kinase-type cell surface receptor her2) (mln 19). [swissprot;acc:p04626]
similar to kinase suppressor of ras (fragment). [sptrembl;acc:q8ivt5] Divided 5880.37 6334.71 1.07726
1430 dual specificity mitogen-activated protein kinase kinase 2 (ec 2.7.1.-) (map kinase kinase 2) (mapkk 2) (erk activator kinase 2) (mapk/erk kinase 2) (mek2). [swissprot;acc:p36507]
transducin beta-like 3; wd-repeat protein sazd. [refseq;acc:nm_006453] Subtracted 4025.3 4474.3 449
1431 limkain beta 2. [refseq;acc:nm_025140] Divided 5796.03 6243.78 1.07725
lin-7 homolog c; lin-7 protein 3. [refseq;acc:nm_018362] Subtracted 5743.26 6191.96 448.7
1432 glutaminyl-trna synthetase (ec 6.1.1.18) (glutamine--trna ligase) (glnrs). [swissprot;acc:p47897] 5500.92 5949.26 448.34
zinc finger protein zic 2 (zinc finger protein of the cerebellum 2). [swissprot;acc:o95409] Divided 5658.58 6095.62 1.07723
1433 dna topoisomerase iii alpha (ec 5.99.1.2). [swissprot;acc:q13472] 5692.34 6131.71 1.07719
spermidine synthase (ec 2.5.1.16) (putrescine aminopropyltransferase) (spdsy). [swissprot;acc:p19623] Subtracted 5500.92 5949.26 448.34
1434 glycyl-trna synthetase (ec 6.1.1.14) (glycine--trna ligase) (glyrs). [swissprot;acc:p41250]
myosin viia. [swissprot;acc:q13402] Divided 5759.68 6203.63 1.07708
1435 glutamyl trna synthetase. [sptrembl;acc:o14563] Subtracted 5500.92 5949.26 448.34
ubiquitin-conjugating enzyme e2 b (ec 6.3.2.19) (ubiquitin-protein ligase b) (ubiquitin carrier protein b) (hr6b) (hhr6b) (e2-17 kda). [swissprot;acc:p23567] Divided 5759.68 6203.63 1.07708
1436 casein kinase ii, alpha chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19138] Subtracted 4307.12 4755.03 447.91
ubiquitin-conjugating enzyme e2 a (ec 6.3.2.19) (ubiquitin-protein ligase a) (ubiquitin carrier protein a) (hr6a) (hhr6a). [swissprot;acc:p49459] Divided 5759.68 6203.63 1.07708
1437 casein kinase ii, alpha' chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19784] Subtracted 4307.12 4755.03 447.91
glycerol-3-phosphate dehydrogenase, mitochondrial precursor (ec 1.1.99.5) (gpd-m) (gpdh-m). [swissprot;acc:p43304] Divided 6089.43 6558.02 1.07695
1438 b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] Subtracted 3886.62 3438.82 447.8
exocyst complex component sec10 (hsec10). [swissprot;acc:o00471] Divided 6721.25 7238.34 1.07693
1439 camp response element-binding protein cre-bpa. [refseq;acc:nm_004904] 5658.8 6093.56 1.07683
limkain beta 2. [refseq;acc:nm_025140] Subtracted 5796.03 6243.78 447.75
1440 acyl-coa dehydrogenase, short/branched chain specific, mitochondrial precursor (ec 1.3.99.-) (sbcad) (2-methyl branched chain acyl-coa dehydrogenase) (2-mebcad) (2-methylbutyryl-coenzyme a dehydrogenase) (2-methylbutyryl-coa dehydrogenase). [swissprot;acc:p45954] 6296.52 6743.85 447.33

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/