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 2808 to 2857 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1404 mesoderm induction early response 1. [refseq;acc:nm_020948] Divided 6291.89 6781.6 1.07783
1405 glycerol kinase, testis specific 1 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14409] Subtracted 6137.24 6589.72 452.48
proteasome subunit alpha type 3 (ec 3.4.25.1) (proteasome component c8) (macropain subunit c8) (multicatalytic endopeptidase complex subunit c8). [swissprot;acc:p25788] Divided 6291.89 6781.6 1.07783
1406 glycerol kinase (ec 2.7.1.30) (atp:glycerol 3-phosphotransferase) (glycerokinase) (gk). [swissprot;acc:p32189] Subtracted 6137.09 6589.57 452.48
ribokinase (ec 2.7.1.15). [swissprot;acc:q9h477] Divided 6210.51 6693.49 1.07777
1407 glycerol kinase, testis specific 2 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14410] Subtracted 6137.53 6590.01 452.48
transketolase (ec 2.2.1.1) (tk). [swissprot;acc:p29401] Divided 5692.53 6134.64 1.07766
1408 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] Subtracted 6079.65 6530.82 451.17
serologically defined colon cancer antigen 16. [refseq;acc:nm_006649] Divided 6268.94 6755.57 1.07763
1409 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 1.07749
proteasome subunit beta type 6 precursor (ec 3.4.25.1) (proteasome delta chain) (macropain delta chain) (multicatalytic endopeptidase complex delta chain) (proteasome subunit y). [swissprot;acc:p28072] Subtracted 6221.35 6672.51 451.16
1410 delta-interacting protein a (hepatitis delta antigen interacting protein a). [swissprot;acc:q15834] Divided 6274.62 6760.78 1.07748
transcriptional adaptor 3-like isoform a. [refseq;acc:nm_006354] Subtracted 7260.23 7711.3 451.07
1411 14-3-3 protein beta/alpha (protein kinase c inhibitor protein-1) (kcip-1) (protein 1054). [swissprot;acc:p31946] Divided 5812.02 6262.07 1.07743
frg1 protein (fshd region gene 1 protein). [swissprot;acc:q14331] Subtracted 7260.23 7711.3 451.07
1412 histone deacetylase 5 (hd5) (antigen ny-co-9). [swissprot;acc:q9uql6] Divided 5813.84 6263.92 1.07742
transcriptional adapter 2-like (ada2-like protein) (kl04p). [swissprot;acc:o75478] Subtracted 7260.23 7711.3 451.07
1413 bromodomain containing 7; bromodomain protein; bromodomain-containing 7. [refseq;acc:nm_013263] 7711.29 451.06
histone deacetylase 9 (hd9) (hd7b) (hd7). [swissprot;acc:q9ukv0] Divided 5813.88 6263.97 1.07742
1414 26s proteasome non-atpase regulatory subunit 6 (26s proteasome regulatory subunit s10) (p42a) (proteasome regulatory particle subunit p44s10). [swissprot;acc:q15008] Subtracted 5984.47 6435.42 450.95
histone deacetylase 4 (hd4). [swissprot;acc:p56524] Divided 5813.88 6263.96 1.07741
1415 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 1.0774
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]

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/