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 4008 to 4057 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
2004 receptor protein-tyrosine kinase erbb-4 precursor (ec 2.7.1.112) (p180erbb4) (tyrosine kinase-type cell surface receptor her4). [swissprot;acc:q15303] Divided 225.019 222.969 1.00919
2005 epidermal growth factor receptor precursor (ec 2.7.1.112) (receptor protein-tyrosine kinase erbb-1). [swissprot;acc:p00533] 222.971
sodium/iodide cotransporter (na(+)/i(-) cotransporter) (sodium-iodide symporter) (na+/i-symporter). [swissprot;acc:q92911] Subtracted 204.682 202.784 1.898
2006 lamin b1. [swissprot;acc:p20700] 218.919 220.813 1.894
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] Divided 225.019 222.971 1.00919
2007 2-hydroxyphytanoyl-coa lyase (ec 4.1.-.-) (2-hpcl) (hspc279). [swissprot;acc:q9uj83] 222.969
centaurin beta 5 (cnt-b5). [swissprot;acc:q96p50] Subtracted 218.919 220.812 1.893
2008 centaurin beta 2 (cnt-b2). [swissprot;acc:q15057]
receptor protein-tyrosine kinase erbb-3 precursor (ec 2.7.1.112) (c-erbb3) (tyrosine kinase-type cell surface receptor her3). [swissprot;acc:p21860] Divided 225.019 222.969 1.00919
2009 centaurin beta 1 (cnt-b1). [swissprot;acc:q15027] Subtracted 218.919 220.812 1.893
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 216.201 214.245 1.00913
2010 kidney and liver proline oxidase 1. [refseq;acc:nm_021232] Subtracted 204.651 202.759 1.892
tubulin-specific chaperone c (tubulin-folding cofactor c) (cfc). [swissprot;acc:q15814] Divided 193.517 191.766 1.00913
2011 lamin a/c (70 kda lamin). [swissprot;acc:p02545] Subtracted 218.92 220.811 1.891
putative acyl-coa thioester hydrolase cgi-16 (ec 3.1.2.-). [swissprot;acc:q9y305] Divided 193.517 191.766 1.00913
2012 dead-box protein. [refseq;acc:nm_018665]
vacuolar protein sorting 33b (hvps33b). [swissprot;acc:q9h267] Subtracted 215.553 213.663 1.89
2013 protein phosphatase 1, regulatory (inhibitor) subunit 12b isoform a; myosin phosphatase regulatory subunit; myosin phosphatase, target subunit 2. [refseq;acc:nm_002481] Divided 217.662 215.693 1.00913
vacuolar protein sorting 11 (hvps11) (pp3476). [swissprot;acc:q9h270] Subtracted 215.553 213.663 1.89
2014 protein phosphatase 1, regulatory (inhibitor) subunit 12a; myosin phosphatase, target subunit 1. [refseq;acc:nm_002480] Divided 217.676 215.709 1.00912
vacuolar protein sorting 33a (hvps33a). [swissprot;acc:q96ax1] Subtracted 215.553 213.663 1.89
2015 dna topoisomerase iii alpha (ec 5.99.1.2). [swissprot;acc:q13472] Divided 217.941 215.979 1.00908
solute carrier family 5 (iodide transporter), member 8; apical iodide transporter. [refseq;acc:nm_145913] Subtracted 204.636 202.748 1.888
2016 electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial precursor (ec 1.5.5.1) (etf-qo) (etf-ubiquinone oxidoreductase) (etf dehydrogenase) (electron-transferring- flavoprotein dehydrogenase). [swissprot;acc:q16134] Divided 199.092 197.301 1.00908
sodium-dependent multivitamin transporter (na(+)-dependent multivitamin transporter). [swissprot;acc:q9y289] Subtracted 204.626 202.739 1.887
2017 histidyl-trna synthetase homolog (ec 6.1.1.21) (histidine--trna ligase homolog) (hisrs). [swissprot;acc:p49590] 187.231 185.349 1.882
ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050] Divided 127.397 128.553 1.00907
2018 histidyl-trna synthetase (ec 6.1.1.21) (histidine--trna ligase) (hisrs). [swissprot;acc:p12081] Subtracted 187.292 185.413 1.879
serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129] Divided 127.397 128.553 1.00907
2019 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] 215.799 213.865 1.00904
solute carrier family 2, facilitated glucose transporter, member 6 (glucose transporter type 6) (glucose transporter type 9). [swissprot;acc:q9ugq3] Subtracted 224.124 226.003 1.879
2020 putative eukaryotic translation initiation factor 3 subunit (eif-3) (fragment). [swissprot;acc:o75153] Divided 223.168 221.176 1.00901
solute carrier family 2, facilitated glucose transporter, member 8 (glucose transporter type 8) (glucose transporter type x1). [swissprot;acc:q9ny64] Subtracted 224.124 226.003 1.879
2021 hexaprenyldihydroxybenzoate methyltransferase, mitochondrial precursor (ec 2.1.1.114) (dihydroxyhexaprenylbenzoate methyltransferase) (3,4- dihydroxy-5-hexaprenylbenzoate methyltransferase) (dhhb methyltransferase) (dhhb-mt) (dhhb-mtase). [swissprot;acc:q9nzj6] Divided 208.601 210.464 1.00893
Subtracted 1.863
2022 atp synthase coupling factor b, mitochondrial precursor. [swissprot;acc:q99766] Divided 1.00893
Subtracted 1.863
2023 guanine deaminase (ec 3.5.4.3) (guanase) (guanine aminase) (guanine aminohydrolase) (gah) (p51-nedasin). [swissprot;acc:q9y2t3] Divided 1.00893
Subtracted 1.863
2024 f-actin capping protein alpha-3 subunit (capz alpha-3) (germ cell- specific protein 3). [swissprot;acc:q96kx2] 215.322 213.46 1.862
vacuolar protein sorting 33b (hvps33b). [swissprot;acc:q9h267] Divided 215.553 213.663 1.00885
2025 alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298] 189.987 191.668
f-actin capping protein beta subunit (capz beta). [swissprot;acc:p47756] Subtracted 215.322 213.46 1.862
2026 ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [refseq;acc:nm_016304] 200.219 198.37 1.849
vacuolar protein sorting 11 (hvps11) (pp3476). [swissprot;acc:q9h270] Divided 215.553 213.663 1.00885
2027 lin-7 homolog c; lin-7 protein 3. [refseq;acc:nm_018362] 225.015 223.041
translation initiation factor eif-2b beta subunit (eif-2b gdp-gtp exchange factor) (s20i15) (s20iii15). [swissprot;acc:p49770] Subtracted 220.787 222.634 1.847
2028 topoisomerase-related function protein 4-2. [refseq;acc:nm_022447] 229.267 227.433 1.834
vacuolar protein sorting 33a (hvps33a). [swissprot;acc:q96ax1] Divided 215.553 213.663 1.00885
2029 cytoplasmic cysteine conjugate-beta lyase; glutamine-phenylpyruvate aminotransferase. [refseq;acc:nm_004059] 189.999 191.677 1.00883

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/