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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Gene Rank expected description measured Hugo final
Results: HTML CSV LaTeX Showing element 2252 to 2301 of 3206 in total
Rank
expected
description
measured
Hugo
final
2252 0.343091 TRANSKETOLASE-LIKE 1 (EC 2.2.1.1) (TRANSKETOLASE 2) (TK 2) (TRANSKETOLASE RELATED PROTEIN). [SWISSPROT;Acc:P51854] 0.0765571 TKTL1 0.223139342
2253 0.267978 PHOSPHATIDYLINOSITOL 3-KINASE REGULATORY GAMMA SUBUNIT (PI3-KINASE P85-GAMMA SUBUNIT) (PTDINS-3-KINASE P85-GAMMA) (P55PIK). [SWISSPROT;Acc:Q92569] 0.0597741 PIK3R3 0.223055997
2254 0.138615 0.0309189 C7orf24 0.223055946
2255 0.389405 STEROL REGULATORY ELEMENT BINDING PROTEIN CLEAVAGE-ACTIVATING PROTEIN (SREBP CLEAVAGE-ACTIVATING PROTEIN) (SCAP). [SWISSPROT;Acc:Q12770] 0.0868591 SCAP 0.223055944
2256 0.266211 PHOSPHATIDYLINOSITOL 3-KINASE REGULATORY ALPHA SUBUNIT (PI3-KINASE P85-ALPHA SUBUNIT) (PTDINS-3-KINASE P85-ALPHA) (PI3K). [SWISSPROT;Acc:P27986] 0.0593799 PIK3R1 0.223055772
2257 0.389405 0.086859 no value 0.223055688
2258 0.251275 PHOSPHATIDYLINOSITOL 3-KINASE REGULATORY BETA SUBUNIT (PI3-KINASE P85-BETA SUBUNIT) (PTDINS-3-KINASE P85-BETA). [SWISSPROT;Acc:O00459] 0.0560483 PIK3R2 0.223055616
2259 0.261082 RING FINGER PROTEIN 38. [RefSeq;Acc:NM_022781] 0.0582358 RNF38 0.223055592
2260 0.240498 RING FINGER PROTEIN 44. [RefSeq;Acc:NM_014901] 0.0536444 RNF44 0.223055493
2261 0.138512 0.0308958 ATPAF1 0.223055042
2262 1.64277 "ATP SYNTHASE BETA CHAIN, MITOCHONDRIAL PRECURSOR (EC 3.6.3.14). [SWISSPROT;Acc:P06576]" 0.366428 ATP5B 0.223054962
2263 0.528749 NEUROTRYPSIN PRECURSOR (EC 3.4.21.-) (MOTOPSIN) (LEYDIN). [SWISSPROT;Acc:P56730] 0.11794 PRSS12 0.223054795
2264 0.784403 RIBONUCLEASE P PROTEIN SUBUNIT P30 (EC 3.1.26.5) (RNASEP PROTEIN P30) (RNASE P SUBUNIT 2). [SWISSPROT;Acc:P78346] 0.174876 RPP30 0.222941524
2265 0.671325 SHWACHMAN-BODIAN-DIAMOND SYNDROME PROTEIN (CGI-97). [SWISSPROT;Acc:Q9Y3A5] 0.149637 SBDS 0.222898
2266 0.239746 TOPOISOMERASE-RELATED FUNCTION PROTEIN 4-2. [RefSeq;Acc:NM_022447] 0.0534133 PAPD5 0.222791204
2267 0.302153 POLYMERASE (DNA DIRECTED) SIGMA; TOPOISOMERASE-RELATED FUNCTION PROTEIN 4-1; POLYMERASE (DNA-DIRECTED) SIGMA. [RefSeq;Acc:NM_006999] 0.0673124 POLS 0.222775878
2268 0.133476 LEUKOTRIENE A-4 HYDROLASE (EC 3.3.2.6) (LTA-4 HYDROLASE) (LEUKOTRIENE A(4) HYDROLASE). [SWISSPROT;Acc:P09960] 0.0297305 LTA4H 0.222740418
2269 1.41191 "DIHYDROOROTATE DEHYDROGENASE, MITOCHONDRIAL PRECURSOR (EC 1.3.3.1) (DIHYDROOROTATE OXIDASE) (DHODEHASE) (FRAGMENT). [SWISSPROT;Acc:Q02127]" 0.314489 DHODH 0.222740118
2270 0.120229 PUROMYCIN-SENSITIVE AMINOPEPTIDASE (EC 3.4.11.-) (PSA). [SWISSPROT;Acc:P55786] 0.0267797 NPEPPS 0.222739106
2271 0.58046 GLYCEROL KINASE (EC 2.7.1.30) (ATP:GLYCEROL 3-PHOSPHOTRANSFERASE) (GLYCEROKINASE) (GK). [SWISSPROT;Acc:P32189] 0.129279 no value 0.222718189
2272 0.591632 "GLYCEROL KINASE, TESTIS SPECIFIC 1 (EC 2.7.1.30) (ATP:GLYCEROL 3- PHOSPHOTRANSFERASE) (GLYCEROKINASE) (GK). [SWISSPROT;Acc:Q14409]" 0.131767 0.222717838
2273 0.615573 "GLYCEROL KINASE, TESTIS SPECIFIC 2 (EC 2.7.1.30) (ATP:GLYCEROL 3- PHOSPHOTRANSFERASE) (GLYCEROKINASE) (GK). [SWISSPROT;Acc:Q14410]" 0.137099 0.222717696
2274 0.822563 MITOCHONDRIAL TRANSLATIONAL RELEASE FACTOR 1-LIKE. [RefSeq;Acc:NM_019041] 0.183185 MTRF1L 0.222700267
2275 1.32025 0.294007 no value 0.2226904
2276 0.249916 MANNOSE-P-DOLICHOL UTILIZATION DEFECT 1 PROTEIN (SUPPRESSOR OF LEC15 AND LEC35 GLYCOSYLATION MUTATION HOMOLOG) (SL15). [SWISSPROT;Acc:O75352] 0.0556491 MPDU1 0.222671218
2277 0.639129 "PEPTIDE CHAIN RELEASE FACTOR 1, MITOCHONDRIAL PRECURSOR (MRF-1). [SWISSPROT;Acc:O75570]" 0.142292 MTRF1 0.222634241
2278 1.55897 DIPHTHAMIDE BIOSYNTHESIS-LIKE PROTEIN 2. [RefSeq;Acc:NM_001384] 0.346955 DPH2 0.222553994
2279 0.687157 0.152886 GDPD3 0.222490639
2280 0.575175 "28S RIBOSOMAL PROTEIN S16, MITOCHONDRIAL PRECURSOR (MRP-S16) (CGI- 132). [SWISSPROT;Acc:Q9Y3D3]" 0.12797 MRPS16 0.222488808
2281 0.229168 14.5 KDA TRANSLATIONAL INHIBITOR PROTEIN (P14.5) (UK114 ANTIGEN HOMOLOG). [SWISSPROT;Acc:P52758] 0.0509775 HRSP12 0.222445978
2282 3.81401 DNA-DIRECTED RNA POLYMERASE II 14.4 KDA POLYPEPTIDE (EC 2.7.7.6) (RPB6) (RPB14.4) (RPABC2). [SWISSPROT;Acc:P41584] 0.848404 POLR2F 0.222444094
2283 0.846836 0.188344 GDPD1 0.222409061
2284 0.813521 APOLIPOPROTEIN A-I BINDING PROTEIN; APOA-I BINDING PROTEIN. [RefSeq;Acc:NM_144772] 0.180926 APOA1BP 0.222398684
2285 1.12113 DNA-DIRECTED RNA POLYMERASE II 13.3 KDA POLYPEPTIDE (EC 2.7.7.6) (RPB11). [SWISSPROT;Acc:P52435] 0.249308 POLR2J 0.222372071
2286 0.662751 0.147358 MAP3K7IP3 0.222342931
2287 0.261739 HOMEOBOX PROTEIN DLX-2. [SWISSPROT;Acc:Q07687] 0.0581957 DLX2 0.222342486
2288 MBD2 (METHYL-CPG-BINDING PROTEIN)-INTERACTING ZINC FINGER PROTEIN. [RefSeq;Acc:NM_015517] MIZF
2289 0.519559 MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 7 INTERACTING PROTEIN 2 ISOFORM 1; TAK1-BINDING PROTEIN 2. [RefSeq;Acc:NM_015093] 0.11552 MAP3K7IP2 0.22234241
2290 0.199308 HOMEOBOX PROTEIN DLX-5. [SWISSPROT;Acc:P56178] 0.0443146 DLX5 0.222342304
2291 0.12283 NEURONAL TROPOMODULIN (N-TMOD) (TROPOMODULIN 2). [SWISSPROT;Acc:Q9NZR1] 0.0273103 TMOD2 0.222342262
2292 0.124173 UBIQUITOUS TROPOMODULIN (U-TMOD) (TROPOMODULIN 3). [SWISSPROT;Acc:Q9NYL9] 0.0276089 TMOD3 0.222342216
2293 0.145189 TROPOMODULIN 1 (ERYTHROCYTE TROPOMODULIN) (E-TMOD). [SWISSPROT;Acc:P28289] 0.0322816 TMOD1 0.222341913
2294 ACTIVATED P21CDC42HS KINASE. [RefSeq;Acc:NM_005781] TNK2
2295 0.123338 SKELETAL MUSCLE TROPOMODULIN (SK-TMOD) (TROPOMODULIN 4). [SWISSPROT;Acc:Q9NZQ9] 0.0274232 TMOD4 0.222341857
2296 0.546564 FETAL BRAIN PROTEIN 239 (239FB). [SWISSPROT;Acc:Q15777] 0.121524 MPPED2 0.222341757
2297 1.06765 SORTING NEXIN 9 (SH3 AND PX DOMAIN-CONTAINING PROTEIN 1) (SDP1 PROTEIN). [SWISSPROT;Acc:Q9Y5X1] 0.237383 SNX9 0.222341591
2298 0.197784 HOMEOBOX PROTEIN DLX-3. [SWISSPROT;Acc:O60479] 0.0439756 DLX3 0.222341544
2299 1.78321 TRANSCRIPTION INITIATION FACTOR TFIID 20/15 KDA SUBUNITS (TAFII- 20/TAFII-15) (TAFII20/TAFII15). [SWISSPROT;Acc:Q16514] 0.396471 TAF12 0.222335563
2300 1.47133 SORTING NEXIN 1. [SWISSPROT;Acc:Q13596] 0.327115 SNX1 0.222326059
2301 0.469849 P10-BINDING PROTEIN. [RefSeq;Acc:NM_024491] 0.10445 CEP70 0.222305464

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/