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 Network Type I Analysis

Type 1 network in which we propagated the absolute log regulation ratio abs(log(r/g)). We used the filtered lowest boundary of the confidence interval for the microarray measurement based and used the high confidence interaction map. Because type-I networks tend to favour highly connected proteins we tested a normalisation scheme in which we would run the network once with real values (the measured column) and once with simulated values where each measured point is set to 1 instead of the actual signal (the expected column). Afterwards we divided the measured value by the expected value. This normalisation scheme works to a certain extend but will lead to a variance that is directly related to the connectivity of each protein. In the end we dropped the use of Type-I networks due to the many technical problems they pose.


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Rank Gene description measured expected final Hugo
Results: HTML CSV LaTeX Showing element 208 to 257 of 3206 in total
Rank
description
measured
expected
final
Hugo
208 ANDROGEN-INDUCED 1; CGI-103 PROTEIN; ANDROGEN INDUCED PROTEIN. [RefSeq;Acc:NM_016108] 0.281345 0.87768 0.320555328 AIG1
209 PHENYLALANINE-4-HYDROXYLASE (EC 1.14.16.1) (PAH) (PHE-4- MONOOXYGENASE). [SWISSPROT;Acc:P00439] 1.48249 4.62476 0.320555013 PAH
210 BA127L20.1 (NOVEL GLUTATHIONE-S-TRANSFERASE). [SPTREMBL;Acc:Q9H4Y5] 0.135419 0.422452 0.320554761 GSTO2
211 GLUTATHIONE TRANSFERASE OMEGA 1 (EC 2.5.1.18) (GSTO 1-1). [SWISSPROT;Acc:P78417] 0.155654 0.485577 0.320554721 GSTO1
212 "ATP SYNTHASE B CHAIN, MITOCHONDRIAL PRECURSOR (EC 3.6.3.14). [SWISSPROT;Acc:P24539]" ATP5F1
213 RD PROTEIN. [SWISSPROT;Acc:P18615] no value
214 J DOMAIN CONTAINING PROTEIN 1. [SWISSPROT;Acc:Q9UKB3] DNAJC12
215 PP3111 PROTEIN. [RefSeq;Acc:NM_022156] DUS1L
216 SORTING NEXIN 13 (RGS DOMAIN- AND PHOX DOMAIN-CONTAINING PROTEIN) (RGS-PX1). [SWISSPROT;Acc:Q9Y5W8] 0.147132 0.458992 0.320554607 SNX13
217 DR1-ASSOCIATED PROTEIN 1; NEGATIVE COFACTOR 2 ALPHA; DR1-ASSOCIATED COREPRESSOR. [RefSeq;Acc:NM_006442] 0.215654 0.675264 0.319362501 DRAP1
218 SMALL NUCLEAR RIBONUCLEOPROTEIN SM D3 (SNRNP CORE PROTEIN D3) (SM-D3). [SWISSPROT;Acc:P43331] 0.923366 2.89146 0.319342478 SNRPD3
219 EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT 10 (EIF-3 THETA) (EIF3 P167) (EIF3 P180) (EIF3 P185) (EIF3A). [SWISSPROT;Acc:Q14152] 0.194219 0.608459 0.319198171 EIF3A
220 EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT 4 (EIF-3 DELTA) (EIF3 P44) (EIF-3 RNA-BINDING SUBUNIT) (EIF3 P42) (EIF3G). [SWISSPROT;Acc:O75821] EIF3G
221 0.535221 1.68161 0.318278911 B9D2
222 SAD1/UNC-84 PROTEIN-LIKE 1. [SWISSPROT;Acc:O94901] 0.240086 0.755227 0.317899122 UNC84A
223 XENOTROPIC AND POLYTROPIC RETROVIRUS RECEPTOR. [RefSeq;Acc:NM_004736] 0.0985042 0.309963 0.317793414 XPR1
224 SMALL NUCLEAR RIBONUCLEOPROTEIN SM D2 (SNRNP CORE PROTEIN D2) (SM-D2). [SWISSPROT;Acc:P43330] 0.978717 3.08483 0.317267726 SNRPD2
225 SPLICING FACTOR 3B SUBUNIT 1 (SPLICEOSOME ASSOCIATED PROTEIN 155) (SAP 155) (SF3B155) (PRE-MRNA SPLICING FACTOR SF3B 155 KDA SUBUNIT). [SWISSPROT;Acc:O75533] 0.764466 2.41141 0.317020333 SF3B1
226 VINCULIN (METAVINCULIN). [SWISSPROT;Acc:P18206] 0.253265 0.799038 0.316962397 VCL
227 KINESIN PROTEIN. [RefSeq;Acc:NM_032559] 0.331603 1.04653 0.316859526 KIF2B
228 NY-REN-62 ANTIGEN (FRAGMENT). [SPTREMBL;Acc:Q9Y590] 0.099292 0.313795 0.316423142 KIF21A
229 KINESIN-LIKE PROTEIN KIF2 (KINESIN-2) (HK2). [SWISSPROT;Acc:O00139] 0.425718 1.34686 0.31608185 KIF2A
230 JUN DIMERIZATION PROTEIN. [RefSeq;Acc:NM_130469] 0.193648 0.614336 0.315215127 no value
231 PROTO-ONCOGENE PROTEIN C-FOS (CELLULAR ONCOGENE FOS) (G0/G1 SWITCH REGULATORY PROTEIN 7). [SWISSPROT;Acc:P01100] FOS
232 FOS-RELATED ANTIGEN 2. [SWISSPROT;Acc:P15408] 0.151666 0.481506 0.314982576 FOSL2
233 PROTEIN FOSB (G0/G1 SWITCH REGULATORY PROTEIN 3). [SWISSPROT;Acc:P53539] 0.149853 0.475769 0.31497008 FOSB
234 FOS-RELATED ANTIGEN 1 (FRA-1). [SWISSPROT;Acc:P15407] 0.144083 0.457513 0.31492657 FOSL1
235 "DNA POLYMERASE EPSILON, CATALYTIC SUBUNIT A (EC 2.7.7.7) (DNA POLYMERASE II SUBUNIT A). [SWISSPROT;Acc:Q07864]" 0.259541 0.824492 0.314788985 POLE
236 IMPORTIN BETA-3 SUBUNIT (KARYOPHERIN BETA-3 SUBUNIT) (RAN-BINDING PROTEIN 5). [SWISSPROT;Acc:O00410] 0.162809 0.517346 0.314700413 RANBP5
237 RAN-GTP BINDING PROTEIN (FRAGMENT). [SPTREMBL;Acc:O60518] 0.151819 0.482771 0.31447415 RANBP6
238 0.887185 2.82668 0.313861137 BTF3L4
239 TRANSCRIPTION FACTOR BTF3 (RNA POLYMERASE B TRANSCRIPTION FACTOR 3). [SWISSPROT;Acc:P20290] 0.737493 2.35516 0.313139235 BTF3
240 "5'-AMP-ACTIVATED PROTEIN KINASE, CATALYTIC ALPHA-1 CHAIN (EC 2.7.1.-) (AMPK ALPHA-1 CHAIN). [SWISSPROT;Acc:Q13131]" 0.547661 1.75288 0.312434964 PRKAA1
241 "5'-AMP-ACTIVATED PROTEIN KINASE, BETA-2 SUBUNIT (AMPK BETA-2 CHAIN). [SWISSPROT;Acc:O43741]" 0.404521 1.29474 0.312434157 PRKAB2
242 "5'-AMP-ACTIVATED PROTEIN KINASE, GAMMA-1 SUBUNIT (AMPK GAMMA-1 CHAIN) (AMPKG). [SWISSPROT;Acc:P54619]" 0.180475 0.577642 0.312433999 PRKAG1
243 "5'-AMP-ACTIVATED PROTEIN KINASE, GAMMA-3 SUBUNIT (AMPK GAMMA-3 CHAIN) (AMPK GAMMA3). [SWISSPROT;Acc:Q9UGI9]" 0.177169 0.567061 0.312433759 PRKAG3
244 "5'-AMP-ACTIVATED PROTEIN KINASE, CATALYTIC ALPHA-2 CHAIN (EC 2.7.1.-) (AMPK ALPHA-2 CHAIN). [SWISSPROT;Acc:P54646]" 0.630538 2.01815 0.312433664 PRKAA2
245 "5'-AMP-ACTIVATED PROTEIN KINASE, GAMMA-2 SUBUNIT (AMPK GAMMA-2 CHAIN) (AMPK GAMMA2) (H91620P). [SWISSPROT;Acc:Q9UGJ0]" 0.221131 0.70777 0.312433418 PRKAG2
246 "5'-AMP-ACTIVATED PROTEIN KINASE, BETA-1 SUBUNIT (AMPK BETA-1 CHAIN) (AMPKB). [SWISSPROT;Acc:Q9Y478]" 0.355846 1.13895 0.312433382 PRKAB1
247 TRANSCRIPTION FACTOR BTF3 HOMOLOG 3. [SWISSPROT;Acc:Q13892] 0.625831 2.00343 0.312379769 no value
248 PXR2B PROTEIN. [RefSeq;Acc:NM_016559] 0.253658 0.812851 0.312059652 PEX5L
249 NASCENT-POLYPEPTIDE-ASSOCIATED COMPLEX ALPHA POLYPEPTIDE. [RefSeq;Acc:NM_005594] 0.804734 2.57998 0.311914821 no value
250 ALPHA-NAC PROTEIN. [SPTREMBL;Acc:Q9H009] 0.755644 2.42272 0.311899023
251 0.743299 2.38318 0.311893772
252 SMALL GTP-BINDING TUMOR SUPPRESSOR 1. [RefSeq;Acc:NM_145173] 0.168031 0.538752 0.311889329 DIRAS1
253 DI-RAS2. [RefSeq;Acc:NM_017594] 0.210781 0.675823 0.311887876 DIRAS2
254 0.604572 1.93876 0.311834368 NACAD
255 EXOCYST COMPLEX COMPONENT SEC10 (HSEC10). [SWISSPROT;Acc:O00471] 0.249321 0.799962 0.311666054 EXOC5
256 "NUCLEOLAR PROTEIN FAMILY A, MEMBER 1; GAR1 PROTEIN. [RefSeq;Acc:NM_018983]" 0.11305 0.363171 0.311285868 NOLA1
257 "TRANSCRIPTION FACTOR IIIB 90 KDA SUBUNIT (TFIIIB90) (HTFIIIB90) (B- RELATED FACTOR 1) (HBRF) (TATA BOX-BINDING PROTEIN-ASSOCIATED FACTOR, RNA POLYMERASE III, SUBUNIT 2) (TAF3B2). [SWISSPROT;Acc:Q92994]" 0.0376832 0.121057 0.311284767 BRF1

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 bloody hugo identifier as demanded by the BMC Bioinformatics idiots
- http://analysis.yellowcouch.org/