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 1958 to 2007 of 3206 in total
Rank
description
measured
expected
final
Hugo
1958 "60S RIBOSOMAL PROTEIN L12, MITOCHONDRIAL PRECURSOR (L12MT) (5C5-2). [SWISSPROT;Acc:P52815]" 1.09511 4.73611 0.231225626 MRPL12
1959 NUDIX (NUCLEOSIDE DIPHOSPHATE LINKED MOIETY X)-TYPE MOTIF 12. [RefSeq;Acc:NM_031438] 0.0196941 0.085173 0.231224684 NUDT12
1960 PROTEIN 1-4 (ATP BINDING PROTEIN ASSOCIATED WITH CELL DIFFERENTIATION). [SWISSPROT;Acc:O14530] 0.0389372 0.1684 0.231218527 TXNDC9
1961 ZINC FINGER PROTEIN 291. [SWISSPROT;Acc:Q9BY12] 0.0194686 0.0842001 0.231218253 SCAPER
1962 GTP:AMP PHOSPHOTRANSFERASE MITOCHONDRIAL (EC 2.7.4.10) (AK3) (ADENYLATE KINASE 3 ALPHA LIKE 1). [SWISSPROT;Acc:Q9UIJ7] 0.422914 1.82907 0.231218051 AK3
1963 0.0194686 0.0842002 0.231217978 MED11
1964 PEROXISOME BIOGENESIS FACTOR 1 (PEROXIN-1) (PEROXISOME BIOGENESIS DISORDER PROTEIN 1). [SWISSPROT;Acc:O43933] PEX1
1965 UMP-CMP KINASE (EC 2.7.4.14) (CYTIDYLATE KINASE) (DEOXYCYTIDYLATE KINASE) (CYTIDINE MONOPHOSPHATE KINASE). [SWISSPROT;Acc:P30085] 0.403445 1.74487 0.231217798 CMPK
1966 SURFEIT LOCUS PROTEIN 5. [SWISSPROT;Acc:Q15528] 0.0936292 0.40494 0.231217464 MED22
1967 "ADENYLATE KINASE ISOENZYME 4, MITOCHONDRIAL (EC 2.7.4.3) (ATP-AMP TRANSPHOSPHORYLASE). [SWISSPROT;Acc:P27144]" 0.355425 1.53719 0.231217351 no value
1968 60S RIBOSOMAL PROTEIN L5. [SWISSPROT;Acc:P46777] 1.41778 6.13294 0.231174608 RPL5
1969 DNA-DIRECTED RNA POLYMERASE III LARGEST SUBUNIT (EC 2.7.7.6) (RPC155) (RPC1). [SWISSPROT;Acc:O14802] 0.677997 2.9329 0.231169491 POLR3A
1970 40S RIBOSOMAL PROTEIN S9. [SWISSPROT;Acc:P46781] 0.305347 1.32095 0.231157122 RPS9
1971 60S RIBOSOMAL PROTEIN L30. [SWISSPROT;Acc:P04645] 0.177407 0.767511 0.231145873 RPL30
1972 RNA POLYMERASE I ASSOCIATED FACTOR 53. [RefSeq;Acc:NM_022490] 0.0824177 0.356578 0.231135123 POLR1E
1973 DNA REPAIR PROTEIN RAD51 HOMOLOG 1 (HRAD51) (HSRAD51). [SWISSPROT;Acc:Q06609] 0.407104 1.76144 0.231119993 RAD51
1974 KCCR13L. [RefSeq;Acc:NM_139179] 0.0305909 0.13236 0.231118918 DAGLB
1975 0.023532 0.101818 0.23111827 DAGLA
1976 DNA POLYMERASE DELTA P38 SUBUNIT. [RefSeq;Acc:NM_015584] 0.0281946 0.122012 0.231080549 POLDIP2
1977 "ATP-DEPENDENT CLP PROTEASE ATP-BINDING SUBUNIT CLPX-LIKE, MITOCHONDRIAL PRECURSOR. [SWISSPROT;Acc:O76031]" 0.139859 0.605241 0.231079851 CLPX
1978 MITOCHONDRIAL RIBOSOMAL PROTEIN L17; LYST-INTERACTING PROTEIN LIP2. [RefSeq;Acc:NM_022061] 1.18829 5.14358 0.231023917 MRPL17
1979 60S RIBOSOMAL PROTEIN L10A (CSA-19). [SWISSPROT;Acc:P53025] 0.541146 2.34239 0.231023015 no value
1980 "60S RIBOSOMAL PROTEIN L36, MITOCHONDRIAL PRECURSOR (L36MT) (BRCA1- INTERACTING PROTEIN 1). [SWISSPROT;Acc:Q9P0J6]" 1.23017 5.32517 0.231010465 MRPL36
1981 60S RIBOSOMAL PROTEIN L10 (QM PROTEIN) (TUMOR SUPPRESSOR QM) (LAMININ RECEPTOR HOMOLOG). [SWISSPROT;Acc:P27635] 1.03026 4.4602 0.230989642 no value
1982 RIBOSOMAL PROTEIN L10-LIKE PROTEIN. [RefSeq;Acc:NM_080746] 1.00219 4.3387 0.230988545 RPL10L
1983 DNA-DIRECTED RNA POLYMERASE I LARGEST SUBUNIT (EC 2.7.7.6) (RNA POLYMERASE I 194 KDA SUBUNIT) (RPA194). [SWISSPROT;Acc:O95602] 0.661854 2.86554 0.230970079 POLR1A
1984 EPOXIDE HYDROLASE 1 (EC 3.3.2.3) (MICROSOMAL EPOXIDE HYDROLASE) (EPOXIDE HYDRATASE). [SWISSPROT;Acc:P07099] 0.160147 0.693413 0.230954712 EPHX1
1985 "28S RIBOSOMAL PROTEIN S12, MITOCHONDRIAL PRECURSOR (MPR-S12) (MT- RPS12). [SWISSPROT;Acc:O15235]" 0.485913 2.1041 0.230936267 MRPS12
1986 40S RIBOSOMAL PROTEIN S23. [SWISSPROT;Acc:P39028] RPS23
1987 60S RIBOSOMAL PROTEIN L12. [SWISSPROT;Acc:P30050] 0.527851 2.28589 0.230917061 no value
1988 DJ999L4.1 (NOVEL PROTEIN SIMILAR TO RIBOSOMAL PROTEIN L12 (RPL12)). [SPTREMBL;Acc:Q9NQ02] 0.512921 2.22124 0.230916515
1989 60S RIBOSOMAL PROTEIN L12 LIKE PROTEIN. [SPTREMBL;Acc:O60886] 0.505323 2.18834 0.230916128
1990 DNA-DIRECTED RNA POLYMERASE II LARGEST SUBUNIT (EC 2.7.7.6) (RPB1). [SWISSPROT;Acc:P24928] 0.525129 2.27455 0.230871601 POLR2A
1991 HYALURONAN SYNTHASE 3 (EC 2.4.1.212) (HYALURONATE SYNTHASE 3) (HYALURONIC ACID SYNTHASE 3) (HA SYNTHASE 3). [SWISSPROT;Acc:O00219] 0.0223215 0.0966924 0.230850615 HAS3
1992 HYALURONAN SYNTHASE 1 (EC 2.4.1.212) (HYALURONATE SYNTHASE 1) (HYALURONIC ACID SYNTHASE 1) (HA SYNTHASE 1) (HUHAS1). [SWISSPROT;Acc:Q92839] 0.0190828 0.0826631 0.230850283 HAS1
1993 HYALURONAN SYNTHASE 2 (EC 2.4.1.212) (HYALURONATE SYNTHASE 2) (HYALURONIC ACID SYNTHASE 2) (HA SYNTHASE 2). [SWISSPROT;Acc:Q92819] 0.0203563 0.0881799 0.230849661 HAS2
1994 0.22609 0.979382 0.230849658 DOHH
1995 INTEGRAL MEMBRANE PROTEIN CII-3B. [SPTREMBL;Acc:O75609] 0.221383 0.959291 0.230777731 no value
1996 "SUCCINATE DEHYDROGENASE CYTOCHROME B560 SUBUNIT, MITOCHONDRIAL PRECURSOR (INTEGRAL MEMBRANE PROTEIN CII-3) (QPS1) (QPS-1) (SUCCINATE DEHYDROGENASE COMPLEX SUBUNIT C) (SUCCINATE-UBIQUINONE OXIDOREDUCTASE CYTOCHROME B LARGE SUBUNIT) (CYBL). [SWISSPRO" 0.240428 1.04189 0.230761405 SDHC
1997 40S RIBOSOMAL PROTEIN S14 (PRO2640). [SWISSPROT;Acc:P06366] 0.543161 2.35379 0.230760178 RPS14
1998 40S RIBOSOMAL PROTEIN S18 (KE-3) (KE3). [SWISSPROT;Acc:P25232] no value
1999 METHIONINE AMINOPEPTIDASE 1 (EC 3.4.11.18) (METAP 1) (MAP 1) (PEPTIDASE M 1). [SWISSPROT;Acc:P53582] 0.445085 1.92889 0.230746699 METAP1
2000 METHIONINE AMINOPEPTIDASE 2 (EC 3.4.11.18) (METAP 2) (PEPTIDASE M 2) (INITIATION FACTOR 2 ASSOCIATED 67 KDA GLYCOPROTEIN) (P67) (P67EIF2). [SWISSPROT;Acc:P50579] METAP2
2001 POLY (ADP-RIBOSE) GLYCOHYDROLASE. [RefSeq;Acc:NM_003631] 0.0320499 0.138898 0.230744143 no value
2002 0.029603 0.128294 0.230743449
2003 0.0937028 0.406091 0.230743356 TXNDC10
2004 MTO1 PROTEIN HOMOLOG (CGI-02). [SWISSPROT;Acc:Q9Y2Z2] 0.297474 1.2892 0.230743096 MTO1
2005 40S RIBOSOMAL PROTEIN S20. [SWISSPROT;Acc:P17075] 0.834926 3.6186 0.230731775 RPS20
2006 "HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-9 SPECIFIC 1 (EC 2.1.1.43) (HISTONE H3-K9 METHYLTRANSFERASE 1) (H3-K9-HMTASE 1) (SUPPRESSOR OF VARIEGATION 3-9 HOMOLOG 1) (SU(VAR)3-9 HOMOLOG 1). [SWISSPROT;Acc:O43463]" 0.027437 0.118935 0.230689032 SUV39H1
2007 EUKARYOTIC TRANSLATION INITIATION FACTOR 2 SUBUNIT 1 (EUKARYOTIC TRANSLATION INITIATION FACTOR 2 ALPHA SUBUNIT) (EIF-2-ALPHA) (EIF- 2ALPHA) (EIF-2A). [SWISSPROT;Acc:P05198] 0.761536 3.30114 0.230688792 EIF2S1

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/