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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene description measured expected final Hugo
Results: HTML CSV LaTeX Showing element 1252 to 1301 of 3206 in total
Rank
description
measured
expected
final
Hugo
1252 METHYLENETETRAHYDROFOLATE REDUCTASE (EC 1.5.1.20). [SWISSPROT;Acc:P42898] 0.121247 0.490121 0.247381769 MTHFR
1253 IMPORTIN 4. [RefSeq;Acc:NM_024658] 0.572386 2.31408 0.247349271 no value
1254 SERINE/THREONINE PROTEIN KINASE 13 (EC 2.7.1.37) (AURORA/IPL1/EG2 PROTEIN 2) (AURORA/IPL1-RELATED KINASE 3) (AURORA-C). [SWISSPROT;Acc:Q9UQB9] 0.0283804 0.114745 0.247334524 AURKC
1255 SERINE/THREONINE KINASE 6 (EC 2.7.1.37) (SERINE/THREONINE KINASE 15) (AURORA/IPL1-RELATED KINASE 1) (AURORA-RELATED KINASE 1) (HARK1) (AURORA-A) (BREAST-TUMOR-AMPLIFIED KINASE). [SWISSPROT;Acc:O14965] 0.0366317 0.148106 0.247334342 AURKA
1256 "CYLINDROMATOSIS (TURBAN TUMOR SYNDROME); CYLINDROMATOSIS 1, TURBAN TUMOR SYNDROME. [RefSeq;Acc:NM_015247]" CYLD
1257 SERINE/THREONINE PROTEIN KINASE 12 (EC 2.7.1.37) (AURORA- AND IPL1- LIKE MIDBODY-ASSOCIATED PROTEIN 1) (AIM-1) (AURORA/IPL1-RELATED KINASE 2) (AURORA-RELATED KINASE 2) (STK-1) (AURORA-B). [SWISSPROT;Acc:Q96GD4] 0.0285544 0.115449 0.247333455 AURKB
1258 KINESIN-LIKE PROTEIN KIF23 (MITOTIC KINESIN-LIKE PROTEIN-1) (KINESIN- LIKE PROTEIN 5). [SWISSPROT;Acc:Q02241] 0.310673 1.25609 0.247333392 KIF23
1259 0.0339667 0.137332 0.247332741 AQR
1260 ISCHEMIA/REPERFUSION INDUCIBLE PROTEIN. [RefSeq;Acc:NM_024640] 0.0999509 0.404396 0.247160951 no value
1261 0.12467 0.504447 0.24714192
1262 0.0311675 0.126112 0.24714143 SHQ1
1263 0.110103 0.445662 0.247054943 C9orf7
1264 LAMIN B2. [SWISSPROT;Acc:Q03252] 0.481793 1.95026 0.247040395 no value
1265 BLOCK OF PROLIFERATION 1. [SWISSPROT;Acc:Q14137] 0.872123 3.53236 0.246895277 BOP1
1266 U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM8. [SWISSPROT;Acc:O95777] 0.115741 0.46893 0.246819355 LSM8
1267 NUCLEOLAR RNA-ASSOCIATED PROTEIN ALPHA ISOFORM. [RefSeq;Acc:NM_022917] 0.966893 3.91912 0.246711762 NOL6
1268 SINGLE-MINDED HOMOLOG 1. [SWISSPROT;Acc:P81133] 0.0318532 0.12912 0.246694548 SIM1
1269 PERIPHERAL PLASMA MEMBRANE PROTEIN CASK (EC 2.7.1.-) (HCASK) (CALCIUM/CALMODULIN-DEPENDENT SERINE PROTEIN KINASE) (LIN-2 HOMOLOG). [SWISSPROT;Acc:O14936] 0.685788 2.77992 0.24669343 CASK
1270 HYPOXIA-INDUCIBLE FACTOR-3 ALPHA ISOFORM A; INHIBITORY PAS DOMAIN PROTEIN. [RefSeq;Acc:NM_152794] 0.0415296 0.168345 0.246693397 HIF3A
1271 0.264834 1.07406 0.246572817 no value
1272 I-KAPPA-B-INTERACTING RAS-LIKE PROTEIN 2. [RefSeq;Acc:NM_017595] 0.0342893 0.139064 0.246572082 NKIRAS2
1273 KAPPA B-RAS 1. [RefSeq;Acc:NM_020345] 0.0384625 0.155989 0.246571874 no value
1274 SNARE ASSOCIATED PROTEIN SNAPIN. [RefSeq;Acc:NM_012437] SNAPAP
1275 PROTEASOME SUBUNIT BETA TYPE 9 PRECURSOR (EC 3.4.25.1) (PROTEASOME CHAIN 7) (MACROPAIN CHAIN 7) (MULTICATALYTIC ENDOPEPTIDASE COMPLEX CHAIN 7) (RING12 PROTEIN) (LOW MOLECULAR MASS PROTEIN 2). [SWISSPROT;Acc:P28065] 0.122196 0.495798 0.246463277 no value
1276 "MAGUK P55 SUBFAMILY MEMBER 2 (MPP2 PROTEIN) (DISCS, LARGE HOMOLOG 2). [SWISSPROT;Acc:Q14168]" 0.123807 0.50235 0.246455658 MPP2
1277 MAGUK P55 SUBFAMILY MEMBER 6 (VELI-ASSOCIATED MAGUK 1) (VAM-1). [SWISSPROT;Acc:Q9NZW5] 0.143838 0.583751 0.246403004 MPP6
1278 MYB PROTO-ONCOGENE PROTEIN (C-MYB). [SWISSPROT;Acc:P10242] 0.139096 0.564523 0.24639563 MYB
1279 EPSIN 1; EH DOMAIN-BINDING MITOTIC PHOSPHOPROTEIN. [RefSeq;Acc:NM_013333] 0.0423484 0.171872 0.246394992 EPN1
1280 CALRETICULIN PRECURSOR (CRP55) (CALREGULIN) (HACBP) (ERP60). [SWISSPROT;Acc:P27797] 0.205692 0.834998 0.246338315 CALR
1281 CATHEPSIN B PRECURSOR (EC 3.4.22.1) (CATHEPSIN B1) (APP SECRETASE). [SWISSPROT;Acc:P07858] 0.264212 1.07259 0.246330844 CTSB
1282 CYSTEINE-RICH MOTOR NEURON 1; CYSTEINE-RICH REPEAT-CONTAINING PROTEIN S52 PRECURSOR. [RefSeq;Acc:NM_016441] 0.516861 2.10021 0.246099676 CRIM1
1283 "NUCLEOSTEMIN; PUTATIVE NUCLEOTIDE BINDING PROTEIN, ESTRADIOL-INDUCED. [RefSeq;Acc:NM_014366]" 0.856366 3.47989 0.246089963 GNL3
1284 0.661293 2.68731 0.246079909 GNL3L
1285 0.0982055 0.399189 0.24601254 GPR158
1286 0.0245797 0.0999171 0.246000935 ISCA1
1287 GUANINE NUCLEOTIDE-BINDING PROTEIN-LIKE 1 (GTP-BINDING PROTEIN HSR1). [SWISSPROT;Acc:P36915] 0.129655 0.527051 0.246000861 no value
1288 ZINC FINGER-LIKE PROTEIN 9. [RefSeq;Acc:NM_033414] 0.0473076 0.192307 0.246000406 ZNF622
1289 MEMBRANE-ASSOCIATED TRANSPORTER PROTEIN (AIM-1 PROTEIN) (MELANOMA ANTIGEN AIM1). [SWISSPROT;Acc:Q9UMX9] 0.0493513 0.200615 0.24600005 SLC45A2
1290 60S RIBOSOMAL PROTEIN L19. [SWISSPROT;Acc:P14118] 0.864722 3.51639 0.245911858 RPL19
1291 N-TERMINAL ACETYLTRANSFERASE COMPLEX ARD1 SUBUNIT HOMOLOG (EC 2.3.1.-). [SWISSPROT;Acc:P41227] 0.304267 1.23733 0.245906104 ARD1A
1292 ECOTROPIC VIRAL INTEGRATION SITE 5; NEUROBLASTOMA STAGE 4S GENE. [RefSeq;Acc:NM_005665] 0.0317084 0.128948 0.245900673 EVI5
1293 0.111932 0.455193 0.245900091 C22orf23
1294 0.160447 0.65249 0.245899554 RBMX2
1295 0.0401118 0.163123 0.245899107 BUD13
1296 SIMILAR TO ECOTROPIC VIRAL INTEGRATION SITE 5; NEUROBLASTOMA STAGE 4S GENE. [RefSeq;Acc:NM_145245] EVI5L
1297 0.108852 0.442722 0.245869869 UPRT
1298 0.0760628 0.309407 0.245834128 no value
1299 DELTA-AMINOLEVULINIC ACID DEHYDRATASE (EC 4.2.1.24) (PORPHOBILINOGEN SYNTHASE) (ALADH). [SWISSPROT;Acc:P13716] 0.154288 0.627636 0.245824013 ALAD
1300 BAG-FAMILY MOLECULAR CHAPERONE REGULATOR-3 (BCL-2 BINDING ATHANOGENE- 3) (BAG-3) (BCL-2-BINDING PROTEIN BIS) (DOCKING PROTEIN CAIR-1). [SWISSPROT;Acc:O95817] 0.0975531 0.396904 0.245785127 BAG3
1301 RAC GTPASE ACTIVATING PROTEIN 1; GTPASE ACTIVATING PROTEIN. [RefSeq;Acc:NM_013277] 0.268542 1.09266 0.245769041 RACGAP1

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/