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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2001 to 2050 of 3228 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
red
green
network_comparison
2001 LIN7B 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] 225.02 222.948 1.00929
2002 SNRPB2 u2 small nuclear ribonucleoprotein b". [swissprot;acc:p08579] 214.775 216.769 1.00928
2003 DNALI1 axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645] 208.315 206.41 1.00923
2004 ERBB4 receptor protein-tyrosine kinase erbb-4 precursor (ec 2.7.1.112) (p180erbb4) (tyrosine kinase-type cell surface receptor her4). [swissprot;acc:q15303] 225.019 222.969 1.00919
2005 EGFR epidermal growth factor receptor precursor (ec 2.7.1.112) (receptor protein-tyrosine kinase erbb-1). [swissprot;acc:p00533] 222.971
2006 ERBB2 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]
2007 HACL1 2-hydroxyphytanoyl-coa lyase (ec 4.1.-.-) (2-hpcl) (hspc279). [swissprot;acc:q9uj83] 222.969
2008 ERBB3 receptor protein-tyrosine kinase erbb-3 precursor (ec 2.7.1.112) (c-erbb3) (tyrosine kinase-type cell surface receptor her3). [swissprot;acc:p21860]
2009 CTRL 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] 216.201 214.245 1.00913
2010 TBCC tubulin-specific chaperone c (tubulin-folding cofactor c) (cfc). [swissprot;acc:q15814] 193.517 191.766
2011 ACOT9 putative acyl-coa thioester hydrolase cgi-16 (ec 3.1.2.-). [swissprot;acc:q9y305]
2012 DDX43 dead-box protein. [refseq;acc:nm_018665]
2013 PPP1R12B protein phosphatase 1, regulatory (inhibitor) subunit 12b isoform a; myosin phosphatase regulatory subunit; myosin phosphatase, target subunit 2. [refseq;acc:nm_002481] 217.662 215.693
2014 PPP1R12A protein phosphatase 1, regulatory (inhibitor) subunit 12a; myosin phosphatase, target subunit 1. [refseq;acc:nm_002480] 217.676 215.709 1.00912
2015 TOP3A dna topoisomerase iii alpha (ec 5.99.1.2). [swissprot;acc:q13472] 217.941 215.979 1.00908
2016 ETFDH 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] 199.092 197.301
2017 RRS1 ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050] 127.397 128.553 1.00907
2018 PPP1CA serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129]
2019 no value 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
2020 KIAA0664 putative eukaryotic translation initiation factor 3 subunit (eif-3) (fragment). [swissprot;acc:o75153] 223.168 221.176 1.00901
2021 COQ3 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] 208.601 210.464 1.00893
2022 ATP5S atp synthase coupling factor b, mitochondrial precursor. [swissprot;acc:q99766]
2023 GDA guanine deaminase (ec 3.5.4.3) (guanase) (guanine aminase) (guanine aminohydrolase) (gah) (p51-nedasin). [swissprot;acc:q9y2t3]
2024 VPS33B vacuolar protein sorting 33b (hvps33b). [swissprot;acc:q9h267] 215.553 213.663 1.00885
2025 GPT alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298] 189.987 191.668
2026 VPS11 vacuolar protein sorting 11 (hvps11) (pp3476). [swissprot;acc:q9h270] 215.553 213.663
2027 LIN7C lin-7 homolog c; lin-7 protein 3. [refseq;acc:nm_018362] 225.015 223.041
2028 VPS33A vacuolar protein sorting 33a (hvps33a). [swissprot;acc:q96ax1] 215.553 213.663
2029 CCBL1 cytoplasmic cysteine conjugate-beta lyase; glutamine-phenylpyruvate aminotransferase. [refseq;acc:nm_004059] 189.999 191.677 1.00883
2030 GPT2 alanine aminotransferase 2; glutamic-pyruvate transaminase 2. [refseq;acc:nm_133443]
2031 TTRAP traf and tnf receptor-associated protein; ets1-associated protein 2. [refseq;acc:nm_016614] 218.466 216.562 1.00879
2032 CAPZA3 f-actin capping protein alpha-3 subunit (capz alpha-3) (germ cell- specific protein 3). [swissprot;acc:q96kx2] 215.322 213.46 1.00872
2033 CAPZB f-actin capping protein beta subunit (capz beta). [swissprot;acc:p47756]
2034 CENTB5 centaurin beta 5 (cnt-b5). [swissprot;acc:q96p50] 218.919 220.812 1.00865
2035 CENTB2 centaurin beta 2 (cnt-b2). [swissprot;acc:q15057]
2036 LMNB1 lamin b1. [swissprot;acc:p20700] 220.813
2037 CENTB1 centaurin beta 1 (cnt-b1). [swissprot;acc:q15027] 220.812
2038 LMNA lamin a/c (70 kda lamin). [swissprot;acc:p02545] 218.92 220.811 1.00864
2039 ACSS2 acetyl-coenzyme a synthetase, cytoplasmic (ec 6.2.1.1) (acetate--coa ligase) (acyl-activating enzyme) (acetyl-coa synthetase) (acs) (acecs). [swissprot;acc:q9nr19] 190.551 192.191 1.00861
2040 T brachyury protein (t protein). [swissprot;acc:o15178] 210.586 208.803 1.00854
2041 UBQLN4 ataxin-1 ubiquitin-like interacting protein. [refseq;acc:nm_020131] 196.808 195.141
2042 TBX19 t-box transcription factor tbx19 (t-box protein 19). [swissprot;acc:o60806] 210.586 208.803
2043 UBQLN1 ubiquilin 1 isoform 1. [refseq;acc:nm_013438] 196.837 195.173 1.00853
2044 AP3B1 adapter-related protein complex 3 beta 1 subunit (beta-adaptin 3a) (ap-3 complex beta-3a subunit) (beta-3a-adaptin). [swissprot;acc:o00203] 199.928 198.24 1.00851
2045 C19orf29 ny-ren-24 antigen (fragment). [sptrembl;acc:q9y5a4]
2046 no value adapter-related protein complex 3 beta 2 subunit (beta-adaptin 3b) (ap-3 complex beta-3b subunit) (beta-3b-adaptin) (neuron-specific vesicle coat protein beta-nap). [swissprot;acc:q13367]
2047 SLC2A6 solute carrier family 2, facilitated glucose transporter, member 6 (glucose transporter type 6) (glucose transporter type 9). [swissprot;acc:q9ugq3] 224.124 226.003 1.00838
2048 SLC2A8 solute carrier family 2, facilitated glucose transporter, member 8 (glucose transporter type 8) (glucose transporter type x1). [swissprot;acc:q9ny64]
2049 EIF2B2 translation initiation factor eif-2b beta subunit (eif-2b gdp-gtp exchange factor) (s20i15) (s20iii15). [swissprot;acc:p49770] 220.787 222.634 1.00837
2050 SH3BGR sh3 domain-binding glutamic acid-rich protein (sh3bgr protein) (21- glutamic acid-rich protein) (21-garp). [swissprot;acc:p55822] 218.79 216.981 1.00834

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
- Hugo is the HGNC identifier if it exists
- 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/