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 2258 to 2307 of 3206 in total
Rank
description
measured
expected
final
Hugo
2258 PHOSPHATIDYLINOSITOL 3-KINASE REGULATORY BETA SUBUNIT (PI3-KINASE P85-BETA SUBUNIT) (PTDINS-3-KINASE P85-BETA). [SWISSPROT;Acc:O00459] 0.0560483 0.251275 0.223055616 PIK3R2
2259 RING FINGER PROTEIN 38. [RefSeq;Acc:NM_022781] 0.0582358 0.261082 0.223055592 RNF38
2260 RING FINGER PROTEIN 44. [RefSeq;Acc:NM_014901] 0.0536444 0.240498 0.223055493 RNF44
2261 0.0308958 0.138512 0.223055042 ATPAF1
2262 "ATP SYNTHASE BETA CHAIN, MITOCHONDRIAL PRECURSOR (EC 3.6.3.14). [SWISSPROT;Acc:P06576]" 0.366428 1.64277 0.223054962 ATP5B
2263 NEUROTRYPSIN PRECURSOR (EC 3.4.21.-) (MOTOPSIN) (LEYDIN). [SWISSPROT;Acc:P56730] 0.11794 0.528749 0.223054795 PRSS12
2264 RIBONUCLEASE P PROTEIN SUBUNIT P30 (EC 3.1.26.5) (RNASEP PROTEIN P30) (RNASE P SUBUNIT 2). [SWISSPROT;Acc:P78346] 0.174876 0.784403 0.222941524 RPP30
2265 SHWACHMAN-BODIAN-DIAMOND SYNDROME PROTEIN (CGI-97). [SWISSPROT;Acc:Q9Y3A5] 0.149637 0.671325 0.222898 SBDS
2266 TOPOISOMERASE-RELATED FUNCTION PROTEIN 4-2. [RefSeq;Acc:NM_022447] 0.0534133 0.239746 0.222791204 PAPD5
2267 POLYMERASE (DNA DIRECTED) SIGMA; TOPOISOMERASE-RELATED FUNCTION PROTEIN 4-1; POLYMERASE (DNA-DIRECTED) SIGMA. [RefSeq;Acc:NM_006999] 0.0673124 0.302153 0.222775878 POLS
2268 LEUKOTRIENE A-4 HYDROLASE (EC 3.3.2.6) (LTA-4 HYDROLASE) (LEUKOTRIENE A(4) HYDROLASE). [SWISSPROT;Acc:P09960] 0.0297305 0.133476 0.222740418 LTA4H
2269 "DIHYDROOROTATE DEHYDROGENASE, MITOCHONDRIAL PRECURSOR (EC 1.3.3.1) (DIHYDROOROTATE OXIDASE) (DHODEHASE) (FRAGMENT). [SWISSPROT;Acc:Q02127]" 0.314489 1.41191 0.222740118 DHODH
2270 PUROMYCIN-SENSITIVE AMINOPEPTIDASE (EC 3.4.11.-) (PSA). [SWISSPROT;Acc:P55786] 0.0267797 0.120229 0.222739106 NPEPPS
2271 GLYCEROL KINASE (EC 2.7.1.30) (ATP:GLYCEROL 3-PHOSPHOTRANSFERASE) (GLYCEROKINASE) (GK). [SWISSPROT;Acc:P32189] 0.129279 0.58046 0.222718189 no value
2272 "GLYCEROL KINASE, TESTIS SPECIFIC 1 (EC 2.7.1.30) (ATP:GLYCEROL 3- PHOSPHOTRANSFERASE) (GLYCEROKINASE) (GK). [SWISSPROT;Acc:Q14409]" 0.131767 0.591632 0.222717838
2273 "GLYCEROL KINASE, TESTIS SPECIFIC 2 (EC 2.7.1.30) (ATP:GLYCEROL 3- PHOSPHOTRANSFERASE) (GLYCEROKINASE) (GK). [SWISSPROT;Acc:Q14410]" 0.137099 0.615573 0.222717696
2274 MITOCHONDRIAL TRANSLATIONAL RELEASE FACTOR 1-LIKE. [RefSeq;Acc:NM_019041] 0.183185 0.822563 0.222700267 MTRF1L
2275 0.294007 1.32025 0.2226904 no value
2276 MANNOSE-P-DOLICHOL UTILIZATION DEFECT 1 PROTEIN (SUPPRESSOR OF LEC15 AND LEC35 GLYCOSYLATION MUTATION HOMOLOG) (SL15). [SWISSPROT;Acc:O75352] 0.0556491 0.249916 0.222671218 MPDU1
2277 "PEPTIDE CHAIN RELEASE FACTOR 1, MITOCHONDRIAL PRECURSOR (MRF-1). [SWISSPROT;Acc:O75570]" 0.142292 0.639129 0.222634241 MTRF1
2278 DIPHTHAMIDE BIOSYNTHESIS-LIKE PROTEIN 2. [RefSeq;Acc:NM_001384] 0.346955 1.55897 0.222553994 DPH2
2279 0.152886 0.687157 0.222490639 GDPD3
2280 "28S RIBOSOMAL PROTEIN S16, MITOCHONDRIAL PRECURSOR (MRP-S16) (CGI- 132). [SWISSPROT;Acc:Q9Y3D3]" 0.12797 0.575175 0.222488808 MRPS16
2281 14.5 KDA TRANSLATIONAL INHIBITOR PROTEIN (P14.5) (UK114 ANTIGEN HOMOLOG). [SWISSPROT;Acc:P52758] 0.0509775 0.229168 0.222445978 HRSP12
2282 DNA-DIRECTED RNA POLYMERASE II 14.4 KDA POLYPEPTIDE (EC 2.7.7.6) (RPB6) (RPB14.4) (RPABC2). [SWISSPROT;Acc:P41584] 0.848404 3.81401 0.222444094 POLR2F
2283 0.188344 0.846836 0.222409061 GDPD1
2284 APOLIPOPROTEIN A-I BINDING PROTEIN; APOA-I BINDING PROTEIN. [RefSeq;Acc:NM_144772] 0.180926 0.813521 0.222398684 APOA1BP
2285 DNA-DIRECTED RNA POLYMERASE II 13.3 KDA POLYPEPTIDE (EC 2.7.7.6) (RPB11). [SWISSPROT;Acc:P52435] 0.249308 1.12113 0.222372071 POLR2J
2286 0.147358 0.662751 0.222342931 MAP3K7IP3
2287 HOMEOBOX PROTEIN DLX-2. [SWISSPROT;Acc:Q07687] 0.0581957 0.261739 0.222342486 DLX2
2288 MBD2 (METHYL-CPG-BINDING PROTEIN)-INTERACTING ZINC FINGER PROTEIN. [RefSeq;Acc:NM_015517] MIZF
2289 MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 7 INTERACTING PROTEIN 2 ISOFORM 1; TAK1-BINDING PROTEIN 2. [RefSeq;Acc:NM_015093] 0.11552 0.519559 0.22234241 MAP3K7IP2
2290 HOMEOBOX PROTEIN DLX-5. [SWISSPROT;Acc:P56178] 0.0443146 0.199308 0.222342304 DLX5
2291 NEURONAL TROPOMODULIN (N-TMOD) (TROPOMODULIN 2). [SWISSPROT;Acc:Q9NZR1] 0.0273103 0.12283 0.222342262 TMOD2
2292 UBIQUITOUS TROPOMODULIN (U-TMOD) (TROPOMODULIN 3). [SWISSPROT;Acc:Q9NYL9] 0.0276089 0.124173 0.222342216 TMOD3
2293 TROPOMODULIN 1 (ERYTHROCYTE TROPOMODULIN) (E-TMOD). [SWISSPROT;Acc:P28289] 0.0322816 0.145189 0.222341913 TMOD1
2294 ACTIVATED P21CDC42HS KINASE. [RefSeq;Acc:NM_005781] TNK2
2295 SKELETAL MUSCLE TROPOMODULIN (SK-TMOD) (TROPOMODULIN 4). [SWISSPROT;Acc:Q9NZQ9] 0.0274232 0.123338 0.222341857 TMOD4
2296 FETAL BRAIN PROTEIN 239 (239FB). [SWISSPROT;Acc:Q15777] 0.121524 0.546564 0.222341757 MPPED2
2297 SORTING NEXIN 9 (SH3 AND PX DOMAIN-CONTAINING PROTEIN 1) (SDP1 PROTEIN). [SWISSPROT;Acc:Q9Y5X1] 0.237383 1.06765 0.222341591 SNX9
2298 HOMEOBOX PROTEIN DLX-3. [SWISSPROT;Acc:O60479] 0.0439756 0.197784 0.222341544 DLX3
2299 TRANSCRIPTION INITIATION FACTOR TFIID 20/15 KDA SUBUNITS (TAFII- 20/TAFII-15) (TAFII20/TAFII15). [SWISSPROT;Acc:Q16514] 0.396471 1.78321 0.222335563 TAF12
2300 SORTING NEXIN 1. [SWISSPROT;Acc:Q13596] 0.327115 1.47133 0.222326059 SNX1
2301 P10-BINDING PROTEIN. [RefSeq;Acc:NM_024491] 0.10445 0.469849 0.222305464 CEP70
2302 DNA DIRECTED RNA POLYMERASE II POLYPEPTIDE J-RELATED GENE ISOFORM 3; RPB11B1ALPHA PROTEIN; RPB11B1BETA; DNA-DIRECTED RNA POLYMERASE II SUBUNIT 11. [RefSeq;Acc:NM_032959] 0.231616 1.04193 0.222295164 no value
2303 DNA DIRECTED RNA POLYMERASE II POLYPEPTIDE J-RELATED GENE ISOFORM 1; RPB11B1ALPHA PROTEIN; RPB11B1BETA; DNA-DIRECTED RNA POLYMERASE II SUBUNIT 11. [RefSeq;Acc:NM_145325] 0.232938 1.0479 0.222290295
2304 SERINE PALMITOYLTRANSFERASE 2 (EC 2.3.1.50) (LONG CHAIN BASE BIOSYNTHESIS PROTEIN 2) (LCB 2) (SERINE-PALMITOYL-COA TRANSFERASE 2) (SPT 2). [SWISSPROT;Acc:O15270] 0.0524219 0.235868 0.222251005 SPTLC2
2305 GLUTAMATE CARBOXYPEPTIDASE-LIKE PROTEIN 2 PRECURSOR. [SWISSPROT;Acc:Q96KN2] 0.194519 0.875357 0.222216764 CNDP1
2306 0.25396 1.14298 0.222191114 no value
2307 "GOLGI REASSEMBLY STACKING PROTEIN 2; GOLGI REASSEMBLY STACKING PROTEIN 2, 55 KDA. [RefSeq;Acc:NM_015530]" 0.584026 2.62976 0.222083384 GORASP2

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/