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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final Gene expected measured Rank description Hugo
Results: HTML CSV LaTeX Showing element 902 to 951 of 3206 in total
final
expected
measured
Rank
description
Hugo
0.222216764 0.875357 0.194519 2305 GLUTAMATE CARBOXYPEPTIDASE-LIKE PROTEIN 2 PRECURSOR. [SWISSPROT;Acc:Q96KN2] CNDP1
0.222251005 0.235868 0.0524219 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] SPTLC2
0.222290295 1.0479 0.232938 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] no value
0.222295164 1.04193 0.231616 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]
0.222305464 0.469849 0.10445 2301 P10-BINDING PROTEIN. [RefSeq;Acc:NM_024491] CEP70
0.222326059 1.47133 0.327115 2300 SORTING NEXIN 1. [SWISSPROT;Acc:Q13596] SNX1
0.222335563 1.78321 0.396471 2299 TRANSCRIPTION INITIATION FACTOR TFIID 20/15 KDA SUBUNITS (TAFII- 20/TAFII-15) (TAFII20/TAFII15). [SWISSPROT;Acc:Q16514] TAF12
0.222341544 0.197784 0.0439756 2298 HOMEOBOX PROTEIN DLX-3. [SWISSPROT;Acc:O60479] DLX3
0.222341591 1.06765 0.237383 2297 SORTING NEXIN 9 (SH3 AND PX DOMAIN-CONTAINING PROTEIN 1) (SDP1 PROTEIN). [SWISSPROT;Acc:Q9Y5X1] SNX9
0.222341757 0.546564 0.121524 2296 FETAL BRAIN PROTEIN 239 (239FB). [SWISSPROT;Acc:Q15777] MPPED2
0.222341857 0.123338 0.0274232 2295 SKELETAL MUSCLE TROPOMODULIN (SK-TMOD) (TROPOMODULIN 4). [SWISSPROT;Acc:Q9NZQ9] TMOD4
0.222341913 0.145189 0.0322816 2293 TROPOMODULIN 1 (ERYTHROCYTE TROPOMODULIN) (E-TMOD). [SWISSPROT;Acc:P28289] TMOD1
2294 ACTIVATED P21CDC42HS KINASE. [RefSeq;Acc:NM_005781] TNK2
0.222342216 0.124173 0.0276089 2292 UBIQUITOUS TROPOMODULIN (U-TMOD) (TROPOMODULIN 3). [SWISSPROT;Acc:Q9NYL9] TMOD3
0.222342262 0.12283 0.0273103 2291 NEURONAL TROPOMODULIN (N-TMOD) (TROPOMODULIN 2). [SWISSPROT;Acc:Q9NZR1] TMOD2
0.222342304 0.199308 0.0443146 2290 HOMEOBOX PROTEIN DLX-5. [SWISSPROT;Acc:P56178] DLX5
0.22234241 0.519559 0.11552 2289 MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 7 INTERACTING PROTEIN 2 ISOFORM 1; TAK1-BINDING PROTEIN 2. [RefSeq;Acc:NM_015093] MAP3K7IP2
0.222342486 0.261739 0.0581957 2287 HOMEOBOX PROTEIN DLX-2. [SWISSPROT;Acc:Q07687] DLX2
2288 MBD2 (METHYL-CPG-BINDING PROTEIN)-INTERACTING ZINC FINGER PROTEIN. [RefSeq;Acc:NM_015517] MIZF
0.222342931 0.662751 0.147358 2286 MAP3K7IP3
0.222372071 1.12113 0.249308 2285 DNA-DIRECTED RNA POLYMERASE II 13.3 KDA POLYPEPTIDE (EC 2.7.7.6) (RPB11). [SWISSPROT;Acc:P52435] POLR2J
0.222398684 0.813521 0.180926 2284 APOLIPOPROTEIN A-I BINDING PROTEIN; APOA-I BINDING PROTEIN. [RefSeq;Acc:NM_144772] APOA1BP
0.222409061 0.846836 0.188344 2283 GDPD1
0.222444094 3.81401 0.848404 2282 DNA-DIRECTED RNA POLYMERASE II 14.4 KDA POLYPEPTIDE (EC 2.7.7.6) (RPB6) (RPB14.4) (RPABC2). [SWISSPROT;Acc:P41584] POLR2F
0.222445978 0.229168 0.0509775 2281 14.5 KDA TRANSLATIONAL INHIBITOR PROTEIN (P14.5) (UK114 ANTIGEN HOMOLOG). [SWISSPROT;Acc:P52758] HRSP12
0.222488808 0.575175 0.12797 2280 "28S RIBOSOMAL PROTEIN S16, MITOCHONDRIAL PRECURSOR (MRP-S16) (CGI- 132). [SWISSPROT;Acc:Q9Y3D3]" MRPS16
0.222490639 0.687157 0.152886 2279 GDPD3
0.222553994 1.55897 0.346955 2278 DIPHTHAMIDE BIOSYNTHESIS-LIKE PROTEIN 2. [RefSeq;Acc:NM_001384] DPH2
0.222634241 0.639129 0.142292 2277 "PEPTIDE CHAIN RELEASE FACTOR 1, MITOCHONDRIAL PRECURSOR (MRF-1). [SWISSPROT;Acc:O75570]" MTRF1
0.222671218 0.249916 0.0556491 2276 MANNOSE-P-DOLICHOL UTILIZATION DEFECT 1 PROTEIN (SUPPRESSOR OF LEC15 AND LEC35 GLYCOSYLATION MUTATION HOMOLOG) (SL15). [SWISSPROT;Acc:O75352] MPDU1
0.2226904 1.32025 0.294007 2275 no value
0.222700267 0.822563 0.183185 2274 MITOCHONDRIAL TRANSLATIONAL RELEASE FACTOR 1-LIKE. [RefSeq;Acc:NM_019041] MTRF1L
0.222717696 0.615573 0.137099 2273 "GLYCEROL KINASE, TESTIS SPECIFIC 2 (EC 2.7.1.30) (ATP:GLYCEROL 3- PHOSPHOTRANSFERASE) (GLYCEROKINASE) (GK). [SWISSPROT;Acc:Q14410]" no value
0.222717838 0.591632 0.131767 2272 "GLYCEROL KINASE, TESTIS SPECIFIC 1 (EC 2.7.1.30) (ATP:GLYCEROL 3- PHOSPHOTRANSFERASE) (GLYCEROKINASE) (GK). [SWISSPROT;Acc:Q14409]"
0.222718189 0.58046 0.129279 2271 GLYCEROL KINASE (EC 2.7.1.30) (ATP:GLYCEROL 3-PHOSPHOTRANSFERASE) (GLYCEROKINASE) (GK). [SWISSPROT;Acc:P32189]
0.222739106 0.120229 0.0267797 2270 PUROMYCIN-SENSITIVE AMINOPEPTIDASE (EC 3.4.11.-) (PSA). [SWISSPROT;Acc:P55786] NPEPPS
0.222740118 1.41191 0.314489 2269 "DIHYDROOROTATE DEHYDROGENASE, MITOCHONDRIAL PRECURSOR (EC 1.3.3.1) (DIHYDROOROTATE OXIDASE) (DHODEHASE) (FRAGMENT). [SWISSPROT;Acc:Q02127]" DHODH
0.222740418 0.133476 0.0297305 2268 LEUKOTRIENE A-4 HYDROLASE (EC 3.3.2.6) (LTA-4 HYDROLASE) (LEUKOTRIENE A(4) HYDROLASE). [SWISSPROT;Acc:P09960] LTA4H
0.222775878 0.302153 0.0673124 2267 POLYMERASE (DNA DIRECTED) SIGMA; TOPOISOMERASE-RELATED FUNCTION PROTEIN 4-1; POLYMERASE (DNA-DIRECTED) SIGMA. [RefSeq;Acc:NM_006999] POLS
0.222791204 0.239746 0.0534133 2266 TOPOISOMERASE-RELATED FUNCTION PROTEIN 4-2. [RefSeq;Acc:NM_022447] PAPD5
0.222898 0.671325 0.149637 2265 SHWACHMAN-BODIAN-DIAMOND SYNDROME PROTEIN (CGI-97). [SWISSPROT;Acc:Q9Y3A5] SBDS
0.222941524 0.784403 0.174876 2264 RIBONUCLEASE P PROTEIN SUBUNIT P30 (EC 3.1.26.5) (RNASEP PROTEIN P30) (RNASE P SUBUNIT 2). [SWISSPROT;Acc:P78346] RPP30
0.223054795 0.528749 0.11794 2263 NEUROTRYPSIN PRECURSOR (EC 3.4.21.-) (MOTOPSIN) (LEYDIN). [SWISSPROT;Acc:P56730] PRSS12
0.223054962 1.64277 0.366428 2262 "ATP SYNTHASE BETA CHAIN, MITOCHONDRIAL PRECURSOR (EC 3.6.3.14). [SWISSPROT;Acc:P06576]" ATP5B
0.223055042 0.138512 0.0308958 2261 ATPAF1
0.223055493 0.240498 0.0536444 2260 RING FINGER PROTEIN 44. [RefSeq;Acc:NM_014901] RNF44
0.223055592 0.261082 0.0582358 2259 RING FINGER PROTEIN 38. [RefSeq;Acc:NM_022781] RNF38
0.223055616 0.251275 0.0560483 2258 PHOSPHATIDYLINOSITOL 3-KINASE REGULATORY BETA SUBUNIT (PI3-KINASE P85-BETA SUBUNIT) (PTDINS-3-KINASE P85-BETA). [SWISSPROT;Acc:O00459] PIK3R2
0.223055688 0.389405 0.086859 2257 no value
0.223055772 0.266211 0.0593799 2256 PHOSPHATIDYLINOSITOL 3-KINASE REGULATORY ALPHA SUBUNIT (PI3-KINASE P85-ALPHA SUBUNIT) (PTDINS-3-KINASE P85-ALPHA) (PI3K). [SWISSPROT;Acc:P27986] PIK3R1

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/