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 [...,...].
expected final Gene measured Rank description Hugo
Results: HTML CSV LaTeX Showing element 502 to 551 of 3206 in total
expected
final
measured
Rank
description
Hugo
0.15771 0.228353307 0.0360136 2099 "CYTOCHROME C OXIDASE SUBUNIT IV ISOFORM 2, MITOCHONDRIAL PRECURSOR (EC 1.9.3.1) (COX IV-2). [SWISSPROT;Acc:Q96KJ9]" COX4I2
2100 PEPTIDYL-PROLYL CIS-TRANS ISOMERASE B PRECURSOR (EC 5.2.1.8) (PPIASE) (ROTAMASE) (CYCLOPHILIN B) (S-CYCLOPHILIN) (SCYLP) (CYP-S1). [SWISSPROT;Acc:P23284] PPIB
2101 "CYTOCHROME C OXIDASE SUBUNIT IV ISOFORM 1, MITOCHONDRIAL PRECURSOR (EC 1.9.3.1) (COX IV-1) (CYTOCHROME C OXIDASE POLYPEPTIDE IV). [SWISSPROT;Acc:P13073]" COX4I1
0.157765 0.209999683 0.0331306 2622 MITOGEN-ACTIVATED PROTEIN KINASE 12 (EC 2.7.1.37) (EXTRACELLULAR SIGNAL-REGULATED KINASE 6) (ERK-6) (ERK5) (STRESS-ACTIVATED PROTEIN KINASE-3) (MITOGEN-ACTIVATED PROTEIN KINASE P38 GAMMA) (MAP KINASE P38 GAMMA). [SWISSPROT;Acc:P53778] MAPK11
0.158002 0.278252807 0.0439645 402 CENTAURIN GAMMA 1. [SWISSPROT;Acc:Q99490] CENTG1
0.158229 0.24260281 0.0383868 1509 EXOCYST COMPLEX COMPONENT SEC6. [SWISSPROT;Acc:O60645] EXOC3
0.158312 0.26932513 0.0426374 595 "SPECTRIN BETA CHAIN, BRAIN 1 (SPECTRIN, NON-ERYTHROID BETA CHAIN 1) (BETA-II SPECTRIN) (FODRIN BETA CHAIN). [SWISSPROT;Acc:Q01082]" SPTBN1
0.158511 0.228715357 0.0362539 2091 RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 4 ISOFORM A; APC-STIMULATED GUANINE NUCLEOTIDE EXCHANGE FACTOR. [RefSeq;Acc:NM_015320] ARHGEF4
0.158546 0.243657992 0.038631 1433 RNA HELICASE-RELATED PROTEIN; RNA HELICASE-LIKE PROTEIN; SF3B125 DEAD-BOX PROTEIN. [RefSeq;Acc:NM_007372] no value
0.159183 0.2436573 0.0387861 1435 SPLICING COACTIVATOR SUBUNIT SRM300; RNA BINDING PROTEIN; AT-RICH ELEMENT BINDING FACTOR. [RefSeq;Acc:NM_016333] SRRM2
0.159272 0.2172692 0.0346049 2436 SETD3
0.159275 0.406127139 0.0646859 68 HAIRY/ENHANCER-OF-SPLIT RELATED WITH YRPW MOTIF 1 (HAIRY AND ENHANCER OF SPLIT RELATED-1) (HESR-1) (CARDIOVASCULAR HELIX-LOOP-HELIX FACTOR 2) (HES-RELATED REPRESSOR PROTEIN 2 HERP2). [SWISSPROT;Acc:Q9Y5J3] HEY1
0.15929 0.27107728 0.0431799 543 LRRC4C
0.159487 0.265146376 0.0422874 709 REST COREPRESSOR. [RefSeq;Acc:NM_015156] RCOR1
0.159562 0.411156165 0.0656049 51 LIMKAIN B1. [RefSeq;Acc:NM_019081] KIAA0430
0.159725 0.214767256 0.0343037 2511 C20orf42
0.159817 0.265486775 0.0424293 698 15 KDA SELENOPROTEIN PRECURSOR. [SWISSPROT;Acc:O60613] no value
0.159829 0.245185167 0.0391877 1351 HUMAN IMMUNODEFICIENCY VIRUS TYPE I ENHANCER BINDING PROTEIN 3. [RefSeq;Acc:NM_024503] HIVEP3
0.15995 0.276703345 0.0442587 443 PEROXISOMAL N1-ACETYL-SPERMINE/SPERMIDINE OXIDASE. [RefSeq;Acc:NM_152911] PAOX
0.160098 0.240892453 0.0385664 1578 UPF0183 PROTEIN. [SWISSPROT;Acc:Q9BSU1] C16orf70
0.160453 0.239635283 0.0384502 1616 MAEA
1617 RMND5A
0.160458 0.245522816 0.0393961 1324 "28S RIBOSOMAL PROTEIN S26, MITOCHONDRIAL PRECURSOR (MRP-S26) (MRP- S13). [SWISSPROT;Acc:Q9BYN8]" MRPS26
1325 CHCHD4
0.160664 0.135091869 0.0217044 2999 DOLICHYL-DIPHOSPHOOLIGOSACCHARIDE--PROTEIN GLYCOSYLTRANSFERASE 48 KDA SUBUNIT PRECURSOR (EC 2.4.1.119) (OLIGOSACCHARYL TRANSFERASE 48 KDA SUBUNIT) (DDOST 48 KDA SUBUNIT). [SWISSPROT;Acc:P39656] DDOST
0.160934 0.230298135 0.0370628 2027 SIN3B
0.161679 0.274905832 0.0444465 468 GTP-BINDING PROTEIN ERA HOMOLOG (HERA) (FRAGMENT). [SWISSPROT;Acc:O75616] ERAL1
0.161745 0.249396272 0.0403386 1176 "COP9 SUBUNIT 6 (MOV34 HOMOLOG, 34 KD). [RefSeq;Acc:NM_006833]" COPS6
0.161954 0.239731035 0.0388254 1613 MITOCHONDRIAL RIBOSOMAL PROTEIN L30 ISOFORM A. [RefSeq;Acc:NM_145212] MRPL30
0.162108 0.274304168 0.0444669 478 "SOLUTE CARRIER FAMILY 23, MEMBER 1 (SODIUM-DEPENDENT VITAMIN C TRANSPORTER 1) (HSVCT1) (NA(+)/L-ASCORBIC ACID TRANSPORTER 1) (YOLK SAC PERMEASE-LIKE MOLECULE 3). [SWISSPROT;Acc:Q9UHI7]" SLC23A1
479 SHC TRANSFORMING PROTEIN. [SWISSPROT;Acc:P29353] SHC1
0.162467 0.254565543 0.0413585 1009 C20orf72
0.162737 0.188941052 0.0307477 2860 ORAI1
0.162874 0.475138451 0.0773877 18 FAM49B
0.16302 0.249397007 0.0406567 1166 HISTONE DEACETYLASE 11 (HD11). [SWISSPROT;Acc:Q96DB2] HDAC11
0.163123 0.245899107 0.0401118 1295 BUD13
1296 SIMILAR TO ECOTROPIC VIRAL INTEGRATION SITE 5; NEUROBLASTOMA STAGE 4S GENE. [RefSeq;Acc:NM_145245] EVI5L
0.163279 0.188940403 0.03085 2867 ORAI2
0.163476 0.188940273 0.0308872 2869 PC4 AND SFRS1 INTERACTING PROTEIN 2; PC4 AND SFRS1 INTERACTING PROTEIN 1; TRANSCRIPTIONAL COACTIVATOR P52/P75. [RefSeq;Acc:NM_033222] PSIP1
0.163477 0.251580956 0.0411277 1091 3-OXO-5-ALPHA-STEROID 4-DEHYDROGENASE 1 (EC 1.3.99.5) (STEROID 5-ALPHA-REDUCTASE 1) (SR TYPE 1) (S5AR). [SWISSPROT;Acc:P18405] SRD5A1
0.163636 0.266704148 0.0436424 672 no value
0.163681 0.245185452 0.0401322 1349 HUMAN IMMUNODEFICIENCY VIRUS TYPE I ENHANCER-BINDING PROTEIN 2 (HIV-EP2). [SWISSPROT;Acc:P31629] HIVEP2
0.163741 0.234266311 0.038359 1822 ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 3. [SWISSPROT;Acc:P36405] ARL3
1823 no value
1824 "ANKYRIN 2 (BRAIN ANKYRIN) (ANKYRIN B) (ANKYRIN, NONERYTHROID). [SWISSPROT;Acc:Q01484]" ANK2
0.163819 0.122065817 0.0199967 3010 BRAIN PROTEIN 44. [SWISSPROT;Acc:O95563] BRP44
0.163824 0.240990941 0.0394801 1566 ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 1. [SWISSPROT;Acc:P40616] ARL1
1567 NEFA-INTERACTING NUCLEAR PROTEIN NIP30. [RefSeq;Acc:NM_024946] no value
0.164816 0.279207723 0.0460179 370 "COFILIN, NON-MUSCLE ISOFORM (18 KDA PHOSPHOPROTEIN) (P18). [SWISSPROT;Acc:P23528]" CFL1
371 DESTRIN (ACTIN-DEPOLYMERIZING FACTOR) (ADF). [SWISSPROT;Acc:P18282] DSTN

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/