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 measured description expected final Hugo
Results: HTML CSV LaTeX Showing element 2058 to 2107 of 3206 in total
Rank
measured
description
expected
final
Hugo
2058 0.609415 60S RIBOSOMAL PROTEIN L11. [SWISSPROT;Acc:P39026] 2.65323 0.229687965 RPL11
2059 0.672841 40S RIBOSOMAL PROTEIN S15A. [SWISSPROT;Acc:P39027] 2.92963 0.229667569 RPS15A
2060 0.390544 PROTEIN CGI-27 (C21ORF19-LIKE PROTEIN). [SWISSPROT;Acc:Q9Y316] 1.70053 0.229660165 MEMO1P
2061 0.1548 "GLYCEROL-3-PHOSPHATE DEHYDROGENASE [NAD+], CYTOPLASMIC (EC 1.1.1.8) (GPD-C) (GPDH-C). [SWISSPROT;Acc:P21695]" 0.674093 0.229641904 GPD1
2062 0.476629 26S PROTEASE REGULATORY SUBUNIT 8 (PROTEASOME SUBUNIT P45) (THYROID HORMONE RECEPTOR INTERACTING PROTEIN 1) (TRIP1) (MSUG1 PROTEIN) (TAT-BINDING PROTEIN HOMOLOG 10) (TBP10) (P45/SUG). [SWISSPROT;Acc:P47210] 2.07581 0.229611092 PSMC5
2063 0.0471781 BECLIN 1 (COILED-COIL MYOSIN-LIKE BCL2-INTERACTING PROTEIN) (PROTEIN GT197). [SWISSPROT;Acc:Q14457] 0.20547 0.229610649 BECN1
2064 0.134261 0.584848 0.229565631 GPD1L
2065 0.366443 NUCLEOSIDE DIPHOSPHATE KINASE 3 (EC 2.7.4.6) (NDK 3) (NDP KINASE 3) (NM23-H3) (DR-NM23). [SWISSPROT;Acc:Q13232] 1.59695 0.229464291 NME3
2066 0.16919 "60 KDA HEAT SHOCK PROTEIN, MITOCHONDRIAL PRECURSOR (HSP60) (60 KDA CHAPERONIN) (CPN60) (HEAT SHOCK PROTEIN 60) (HSP-60) (MITOCHONDRIAL MATRIX PROTEIN P1) (P60 LYMPHOCYTE PROTEIN) (HUCHA60). [SWISSPROT;Acc:P10809]" 0.737338 0.229460573 HSPD1
2067 0.016721 RAS-RELATED PROTEIN RAB-26. [SWISSPROT;Acc:Q9ULW5] 0.0728736 0.229452092 RAB26
2068 0.0208556 RAS-RELATED PROTEIN RAB-37. [SWISSPROT;Acc:Q96AX2] 0.0908932 0.229451708 RAB37
2069 0.0584321 0.25466 0.229451425 ZCCHC4
2070 1.60424 DNA-DIRECTED RNA POLYMERASE II 33 KDA POLYPEPTIDE (EC 2.7.7.6) (RPB3) (RNA POLYMERASE II SUBUNIT 3) (RPB33) (RPB31). [SWISSPROT;Acc:P19387] 6.99164 0.229451173 POLR2C
2071 0.130784 "AMINOMETHYLTRANSFERASE, MITOCHONDRIAL PRECURSOR (EC 2.1.2.10) (GLYCINE CLEAVAGE SYSTEM T PROTEIN) (GCVT). [SWISSPROT;Acc:P48728]" 0.569999 0.229446017 AMT
2072 0.640883 "28S RIBOSOMAL PROTEIN S9, MITOCHONDRIAL PRECURSOR (MRP-S9). [SWISSPROT;Acc:P82933]" 2.79379 0.229395552 MRPS9
2073 0.517899 N-ACETYLGLUTAMATE SYNTHASE. [RefSeq;Acc:NM_153006] 2.25773 0.229389254 NAGS
2074 0.411592 SIGNAL RECOGNITION PARTICLE RECEPTOR ALPHA SUBUNIT (SR-ALPHA) (DOCKING PROTEIN ALPHA) (DP-ALPHA). [SWISSPROT;Acc:P08240] 1.79509 0.229287668 no value
2075 0.388695 LIKELY ORTHOLOG OF MOUSE VARIANT POLYADENYLATION PROTEIN CSTF-64. [RefSeq;Acc:NM_015235] 1.69606 0.229175265 CSTF2T
2076 0.299475 PREFOLDIN SUBUNIT 5 (C-MYC BINDING PROTEIN MM-1) (MYC MODULATOR 1). [SWISSPROT;Acc:Q99471] 1.30706 0.229121081 PFDN5
2077 0.027225 PREFOLDIN SUBUNIT 6 (PROTEIN KE2). [SWISSPROT;Acc:O15212] 0.118824 0.22912038 no value
2078 0.374874 LIM/HOMEOBOX PROTEIN LHX4. [SWISSPROT;Acc:Q969G2] 1.63637 0.229088776 LHX4
2079 0.0979801 LIM DOMAIN BINDING 1; CARBOXY TERMINAL LIM DOMAIN PROTEIN 2; LIM DOMAIN-BINDING FACTOR-1. [RefSeq;Acc:NM_003893] 0.427723 0.229073723 no value
2080 0.0881768 LIM DOMAIN BINDING 2; LIM BINDING DOMAIN 2; LIM DOMAIN-BINDING FACTOR-2. [RefSeq;Acc:NM_001290] 0.384928 0.229073489 LDB2
2081 0.0966625 0.421972 0.229073256 C6orf153
2082 0.451026 LIM/HOMEOBOX PROTEIN LHX3. [SWISSPROT;Acc:Q9UBR4] 1.96903 0.229059994 LHX3
2083 0.341867 CAD PROTEIN [INCLUDES: GLUTAMINE-DEPENDENT CARBAMOYL-PHOSPHATE SYNTHASE (EC 6.3.5.5); ASPARTATE CARBAMOYLTRANSFERASE (EC 2.1.3.2); DIHYDROOROTASE (EC 3.5.2.3)]. [SWISSPROT;Acc:P27708] 1.49271 0.229024392 CAD
2084 0.477897 40S RIBOSOMAL PROTEIN S29. [SWISSPROT;Acc:P30054] 2.0867 0.229020463 no value
2085 0.185296 RUVB-LIKE 1 (EC 3.6.1.-) (49-KDA TATA BOX-BINDING PROTEIN-INTERACTING PROTEIN) (49 KDA TBP-INTERACTING PROTEIN) (TIP49A) (PONTIN 52) (NUCLEAR MATRIX PROTEIN 238) (NMP 238) (54 KDA ERYTHROCYTE CYTOSOLIC PROTEIN) (ECP-54) (TIP60-ASSOCIATED PROTEIN 54-ALPHA) 0.809316 0.228953833 RUVBL1
2086 0.149641 "GLUTAMATE DEHYDROGENASE 2, MITOCHONDRIAL PRECURSOR (EC 1.4.1.3) (GDH). [SWISSPROT;Acc:P49448]" 0.654219 0.228732275 GLUD2
2087 "GLUTAMATE DEHYDROGENASE 1, MITOCHONDRIAL PRECURSOR (EC 1.4.1.3) (GDH). [SWISSPROT;Acc:P00367]" GLUDP5
2088 0.031325 0.13696 0.228716414 no value
2089 0.0307532 CDC42 GUANINE EXCHANGE FACTOR 9; HPEM-2 COLLYBISTIN. [RefSeq;Acc:NM_015185] 0.13446 0.228716347 ARHGEF9
2090 0.21824 NUCLEOPORIN LIKE 1. [RefSeq;Acc:NM_014089] 0.954199 0.228715394 NUPL1
2091 0.0362539 RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 4 ISOFORM A; APC-STIMULATED GUANINE NUCLEOTIDE EXCHANGE FACTOR. [RefSeq;Acc:NM_015320] 0.158511 0.228715357 ARHGEF4
2092 0.0601271 "NADPH:ADRENODOXIN OXIDOREDUCTASE, MITOCHONDRIAL PRECURSOR (EC 1.18.1.2) (ADRENODOXIN REDUCTASE) (AR) (FERREDOXIN-NADP(+) REDUCTASE). [SWISSPROT;Acc:P22570]" 0.262913 0.228695804 FDXR
2093 0.313207 "2-OXOGLUTARATE DEHYDROGENASE E1 COMPONENT, MITOCHONDRIAL PRECURSOR (EC 1.2.4.2) (ALPHA-KETOGLUTARATE DEHYDROGENASE). [SWISSPROT;Acc:Q02218]" 1.36954 0.228695036 OGDH
2094 0.282831 1.23673 0.228692601 no value
2095 0.0685085 SYMPLEKIN. [SWISSPROT;Acc:Q92797] 0.299686 0.228600936 SYMPK
2096 0.337171 SIGNAL TRANSDUCING ADAPTOR MOLECULE 2; STAM-LIKE PROTEIN CONTAINING SH3 AND ITAM DOMAINS 2. [RefSeq;Acc:NM_005843] 1.47582 0.228463498 STAM2
2097 0.180388 URIDINE KINASE-LIKE 1. [SWISSPROT;Acc:Q9NWZ5] 0.789739 0.228414704 no value
2098 0.453634 "GLUTATHIONE REDUCTASE, MITOCHONDRIAL PRECURSOR (EC 1.8.1.7) (GR) (GRASE). [SWISSPROT;Acc:P00390]" 1.98642 0.228367616 GSR
2099 0.0360136 "CYTOCHROME C OXIDASE SUBUNIT IV ISOFORM 2, MITOCHONDRIAL PRECURSOR (EC 1.9.3.1) (COX IV-2). [SWISSPROT;Acc:Q96KJ9]" 0.15771 0.228353307 COX4I2
2100 PEPTIDYL-PROLYL CIS-TRANS ISOMERASE B PRECURSOR (EC 5.2.1.8) (PPIASE) (ROTAMASE) (CYCLOPHILIN B) (S-CYCLOPHILIN) (SCYLP) (CYP-S1). [SWISSPROT;Acc:P23284] PPIB
2101 "CYTOCHROME C OXIDASE SUBUNIT IV ISOFORM 1, MITOCHONDRIAL PRECURSOR (EC 1.9.3.1) (COX IV-1) (CYTOCHROME C OXIDASE POLYPEPTIDE IV). [SWISSPROT;Acc:P13073]" COX4I1
2102 0.0653467 0.286165 0.228353223 INTS8
2103 0.0653647 0.286244 0.228353083 GON4L
2104 "PROTEIN KINASE C, EPSILON TYPE (EC 2.7.1.-) (NPKC-EPSILON). [SWISSPROT;Acc:Q02156]" PRKCE
2105 0.173405 UDP-N-ACETYLGLUCOSAMINE--PEPTIDE N-ACETYLGLUCOSAMINYLTRANSFERASE 110 KDA SUBUNIT (EC 2.4.1.-) (O-GLCNAC TRANSFERASE P110 SUBUNIT). [SWISSPROT;Acc:O15294] 0.759373 0.228352865 OGT
2106 0.0507599 "PROTEIN KINASE C, ETA TYPE (EC 2.7.1.-) (NPKC-ETA) (PKC-L). [SWISSPROT;Acc:P24723]" 0.222289 0.228350931 PRKCH
2107 0.0325606 0.142608 0.228322394 FBXO42

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/