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

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/