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

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/