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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Hugo Rank Gene measured description expected final
Results: HTML CSV LaTeX Showing element 101 to 150 of 3206 in total
Hugo  : no value
Rank
measured
description
expected
final
995 0.357881 TRANSDUCIN-LIKE ENHANCER PROTEIN 1 (ESG1). [SWISSPROT;Acc:Q04724] 1.40331 0.255026331
1003 0.0281805 HUNTINGTIN INTERACTING PROTEIN E; HUNTINGTIN INTERACTOR PROTEIN E. [RefSeq;Acc:NM_007076] 0.110551 0.254909499
1015 0.079717 INTERSECTIN 2 (SH3 DOMAIN-CONTAINING PROTEIN 1B) (SH3P18) (SH3P18-LIKE WASP ASSOCIATED PROTEIN). [SWISSPROT;Acc:Q9NZM3] 0.314025 0.253855585
1019 0.0927584 INTERSECTIN 1 (SH3 DOMAIN-CONTAINING PROTEIN 1A) (SH3P17). [SWISSPROT;Acc:Q15811] 0.365399 0.253855101
1024 0.0979873 UBIQUITIN-LIKE PROTEIN SMT3B (SENTRIN 2) (HSMT3). [SWISSPROT;Acc:P55855] 0.386626 0.253442086
1040 0.0397033 "ATP-DEPENDENT DNA HELICASE II, 70 KDA SUBUNIT (LUPUS KU AUTOANTIGEN PROTEIN P70) (KU70) (70 KDA SUBUNIT OF KU ANTIGEN) (THYROID-LUPUS AUTOANTIGEN) (TLAA) (CTC BOX BINDING FACTOR 75 KDA SUBUNIT) (CTCBF) (CTC75). [SWISSPROT;Acc:P12956]" 0.156754 0.253284127
1060 0.398407 GERM CELL-LESS. [RefSeq;Acc:NM_022471] 1.57699 0.25263762
1061 0.294647 PRE-B-CELL LEUKEMIA TRANSCRIPTION FACTOR-2 (HOMEOBOX PROTEIN PBX2) (G17 PROTEIN). [SWISSPROT;Acc:P40425] 1.16629 0.252636137
1075 0.281064 TAX INTERACTION PROTEIN 1. [RefSeq;Acc:NM_014604] 1.11415 0.252267648
1099 0.0322794 PHOSPHOGLYCERATE MUTASE 1 (EC 5.4.2.1) (EC 5.4.2.4) (EC 3.1.3.13) (PHOSPHOGLYCERATE MUTASE ISOZYME B) (PGAM-B) (BPG-DEPENDENT PGAM 1). [SWISSPROT;Acc:P18669] 0.128445 0.251309121
1136 0.199227 PHOSPHOLIPID SCRAMBLASE 3 (PL SCRAMBLASE 3) (CA(2+)-DEPENDENT PHOSPHOLIPID SCRAMBLASE 3). [SWISSPROT;Acc:Q9NRY6] 0.79556 0.250423601
1151 0.0568291 SPROUTY HOMOLOG 4 (SPRY-4). [SWISSPROT;Acc:Q9C004] 0.227574 0.249717015
1161 0.127791 ADAPTER-RELATED PROTEIN COMPLEX 1 SIGMA 1B SUBUNIT (SIGMA-ADAPTIN 1B) (ADAPTOR PROTEIN COMPLEX AP-1 SIGMA-1B SUBUNIT) (GOLGI ADAPTOR HA1/AP1 ADAPTIN SIGMA-1B SUBUNIT) (CLATHRIN ASSEMBLY PROTEIN COMPLEX 1 SIGMA- 1B SMALL CHAIN) (SIGMA 1B SUBUNIT OF AP-1 CL 0.512059 0.249563039
1165 0.144652 "SH2 DOMAIN BINDING PROTEIN 1; TPR-CONTAINING, SH2-BINDING PHOSPHOPROTEIN. [RefSeq;Acc:NM_014633]" 0.579965 0.249415051
1194 0.676836 PROTEASOME SUBUNIT BETA TYPE 8 PRECURSOR (EC 3.4.25.1) (PROTEASOME COMPONENT C13) (MACROPAIN SUBUNIT C13) (MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT C13). [SWISSPROT;Acc:P28062] 2.7231 0.248553487
1196 0.147283 DIHYDROPYRIMIDINE DEHYDROGENASE [NADP+] PRECURSOR (EC 1.3.1.2) (DPD) (DHPDHASE) (DIHYDROURACIL DEHYDROGENASE) (DIHYDROTHYMINE DEHYDROGENASE). [SWISSPROT;Acc:Q12882] 0.5927 0.248495023
1207 0.110079 0.443579 0.248160981
1213 0.0802494 DYSTROPHIN. [SWISSPROT;Acc:P11532] 0.323509 0.24805925
1250 0.11539 BLOCK 23. [SPTREMBL;Acc:Q8NHW5] 0.46643 0.247389748
1251 0.100674 "SIMILAR TO RIBOSOMAL PROTEIN, LARGE, P0. [SPTREMBL;Acc:Q96FQ9]" 0.406955 0.247383617
1253 0.572386 IMPORTIN 4. [RefSeq;Acc:NM_024658] 2.31408 0.247349271
1260 0.0999509 ISCHEMIA/REPERFUSION INDUCIBLE PROTEIN. [RefSeq;Acc:NM_024640] 0.404396 0.247160951
1261 0.12467 0.504447 0.24714192
1264 0.481793 LAMIN B2. [SWISSPROT;Acc:Q03252] 1.95026 0.247040395
1271 0.264834 1.07406 0.246572817
1273 0.0384625 KAPPA B-RAS 1. [RefSeq;Acc:NM_020345] 0.155989 0.246571874
1275 0.122196 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] 0.495798 0.246463277
1287 0.129655 GUANINE NUCLEOTIDE-BINDING PROTEIN-LIKE 1 (GTP-BINDING PROTEIN HSR1). [SWISSPROT;Acc:P36915] 0.527051 0.246000861
1298 0.0760628 0.309407 0.245834128
1316 0.448528 TGF BETA-INDUCIBLE NUCLEAR PROTEIN 1; HAIRY CELL LEUKEMIA PROTEIN 1. [RefSeq;Acc:NM_014886] 1.82552 0.24569876
1322 0.310893 60S ACIDIC RIBOSOMAL PROTEIN P1. [SWISSPROT;Acc:P05386] 1.26602 0.245567211
1328 0.166892 NIF3-LIKE PROTEIN 1 (AMYOTROPHIC LATERAL SCLEROSIS 2 CHROMOSOMAL REGION CANDIDATE GENE PROTEIN 1) (MY018 PROTEIN) (MDS015). [SWISSPROT;Acc:Q9GZT8] 0.679841 0.245486812
1362 0.596229 2.43411 0.244947435
1365 0.0957148 HISTONE H2B.D (H2B/D). [SWISSPROT;Acc:Q99877] 0.390892 0.24486252
1367 0.0942586 HISTONE H2B.E (H2B/E). [SWISSPROT;Acc:Q99879] 0.384945 0.244862513
1368 0.157068 HISTONE H3.1 (H3/A) (H3/C) (H3/D) (H3/F) (H3/H) (H3/I) (H3/J) (H3/K) (H3/L). [SWISSPROT;Acc:P16106] 0.641454 0.244862453
1370 0.0946163 HISTONE H2B.S (H2B/S). [SWISSPROT;Acc:P57053] 0.386406 0.244862399
1371 0.0943097 HISTONE H2B. [RefSeq;Acc:NM_175055] 0.385154 0.244862315
1386 0.037776 BA271B5.1 (SIMILAR TO RIBOSOMAL PROTEIN S7). [SPTREMBL;Acc:Q9H1S9] 0.154523 0.244468461
1390 0.410655 1.68007 0.244427316
1423 0.031639 NUCLEAR RECEPTOR CO-REPRESSOR/HDAC3 COMPLEX SUBUNIT TBLR1 (TBL1- RELATED PROTEIN 1). [SWISSPROT;Acc:Q9BZK7] 0.129724 0.24389473
1431 0.086609 ENTHOPROTIN; EPSIN 4; CLATHRIN INTERACTING PROTEIN LOCALIZED IN THE TRANS-GOLGI REGION. [RefSeq;Acc:NM_014666] 0.355321 0.24374861
1433 0.038631 RNA HELICASE-RELATED PROTEIN; RNA HELICASE-LIKE PROTEIN; SF3B125 DEAD-BOX PROTEIN. [RefSeq;Acc:NM_007372] 0.158546 0.243657992
1448 0.0700456 BASIC PROLINE-RICH PEPTIDE P-E (IB-9). [SWISSPROT;Acc:P02811] 0.287741 0.243432809
1472 0.217383 TRANSCRIPTION FACTOR-LIKE PROTEIN MORF4 (MORTALITY FACTOR 4) (CELLULAR SENESCENCE-RELATED PROTEIN 1) (SEN1). [SWISSPROT;Acc:Q9Y690] 0.894645 0.242982412
1473 0.270547 SURVIVAL MOTOR NEURON PROTEIN (COMPONENT OF GEMS 1) (GEMIN1). [SWISSPROT;Acc:Q16637] 1.11347 0.242976461
1475 0.0733796 RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1 (P21-RAC1) (RAS-LIKE PROTEIN TC25). [SWISSPROT;Acc:P15154] 0.302004 0.24297559
1481 0.0308447 0.126946 0.242974966
1487 0.390142 U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM2 (SMALL NUCLEAR RIBONUCLEAR PROTEIN D HOMOLOG) (G7B) (SNRNP CORE SM-LIKE PROTEIN SM-X5). [SWISSPROT;Acc:Q9Y333] 1.60666 0.242827979
1495 0.036822 IMPORTIN 7; RAN-BINDING PROTEIN 7. [RefSeq;Acc:NM_006391] 0.15167 0.242777082

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/