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 Hugo measured Gene Rank final description
Results: HTML CSV LaTeX Showing element 501 to 550 of 3206 in total
expected
Hugo
measured
Rank
final
description
0.157329 no value 0.0410035 847 0.260622644
0.15771 COX4I1 0.0360136 2101 0.228353307 "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]"
COX4I2 2099 "CYTOCHROME C OXIDASE SUBUNIT IV ISOFORM 2, MITOCHONDRIAL PRECURSOR (EC 1.9.3.1) (COX IV-2). [SWISSPROT;Acc:Q96KJ9]"
PPIB 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]
0.157765 MAPK11 0.0331306 2622 0.209999683 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]
0.158002 CENTG1 0.0439645 402 0.278252807 CENTAURIN GAMMA 1. [SWISSPROT;Acc:Q99490]
0.158229 EXOC3 0.0383868 1509 0.24260281 EXOCYST COMPLEX COMPONENT SEC6. [SWISSPROT;Acc:O60645]
0.158312 SPTBN1 0.0426374 595 0.26932513 "SPECTRIN BETA CHAIN, BRAIN 1 (SPECTRIN, NON-ERYTHROID BETA CHAIN 1) (BETA-II SPECTRIN) (FODRIN BETA CHAIN). [SWISSPROT;Acc:Q01082]"
0.158511 ARHGEF4 0.0362539 2091 0.228715357 RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 4 ISOFORM A; APC-STIMULATED GUANINE NUCLEOTIDE EXCHANGE FACTOR. [RefSeq;Acc:NM_015320]
0.158546 no value 0.038631 1433 0.243657992 RNA HELICASE-RELATED PROTEIN; RNA HELICASE-LIKE PROTEIN; SF3B125 DEAD-BOX PROTEIN. [RefSeq;Acc:NM_007372]
0.159183 SRRM2 0.0387861 1435 0.2436573 SPLICING COACTIVATOR SUBUNIT SRM300; RNA BINDING PROTEIN; AT-RICH ELEMENT BINDING FACTOR. [RefSeq;Acc:NM_016333]
0.159272 SETD3 0.0346049 2436 0.2172692
0.159275 HEY1 0.0646859 68 0.406127139 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]
0.15929 LRRC4C 0.0431799 543 0.27107728
0.159487 RCOR1 0.0422874 709 0.265146376 REST COREPRESSOR. [RefSeq;Acc:NM_015156]
0.159562 KIAA0430 0.0656049 51 0.411156165 LIMKAIN B1. [RefSeq;Acc:NM_019081]
0.159725 C20orf42 0.0343037 2511 0.214767256
0.159817 no value 0.0424293 698 0.265486775 15 KDA SELENOPROTEIN PRECURSOR. [SWISSPROT;Acc:O60613]
0.159829 HIVEP3 0.0391877 1351 0.245185167 HUMAN IMMUNODEFICIENCY VIRUS TYPE I ENHANCER BINDING PROTEIN 3. [RefSeq;Acc:NM_024503]
0.15995 PAOX 0.0442587 443 0.276703345 PEROXISOMAL N1-ACETYL-SPERMINE/SPERMIDINE OXIDASE. [RefSeq;Acc:NM_152911]
0.160098 C16orf70 0.0385664 1578 0.240892453 UPF0183 PROTEIN. [SWISSPROT;Acc:Q9BSU1]
0.160453 MAEA 0.0384502 1616 0.239635283
RMND5A 1617
0.160458 CHCHD4 0.0393961 1325 0.245522816
MRPS26 1324 "28S RIBOSOMAL PROTEIN S26, MITOCHONDRIAL PRECURSOR (MRP-S26) (MRP- S13). [SWISSPROT;Acc:Q9BYN8]"
0.160664 DDOST 0.0217044 2999 0.135091869 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]
0.160934 SIN3B 0.0370628 2027 0.230298135
0.161679 ERAL1 0.0444465 468 0.274905832 GTP-BINDING PROTEIN ERA HOMOLOG (HERA) (FRAGMENT). [SWISSPROT;Acc:O75616]
0.161745 COPS6 0.0403386 1176 0.249396272 "COP9 SUBUNIT 6 (MOV34 HOMOLOG, 34 KD). [RefSeq;Acc:NM_006833]"
0.161954 MRPL30 0.0388254 1613 0.239731035 MITOCHONDRIAL RIBOSOMAL PROTEIN L30 ISOFORM A. [RefSeq;Acc:NM_145212]
0.162108 SHC1 0.0444669 479 0.274304168 SHC TRANSFORMING PROTEIN. [SWISSPROT;Acc:P29353]
SLC23A1 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]"
0.162467 C20orf72 0.0413585 1009 0.254565543
0.162737 ORAI1 0.0307477 2860 0.188941052
0.162874 FAM49B 0.0773877 18 0.475138451
0.16302 HDAC11 0.0406567 1166 0.249397007 HISTONE DEACETYLASE 11 (HD11). [SWISSPROT;Acc:Q96DB2]
0.163123 BUD13 0.0401118 1295 0.245899107
EVI5L 1296 SIMILAR TO ECOTROPIC VIRAL INTEGRATION SITE 5; NEUROBLASTOMA STAGE 4S GENE. [RefSeq;Acc:NM_145245]
0.163279 ORAI2 0.03085 2867 0.188940403
0.163476 PSIP1 0.0308872 2869 0.188940273 PC4 AND SFRS1 INTERACTING PROTEIN 2; PC4 AND SFRS1 INTERACTING PROTEIN 1; TRANSCRIPTIONAL COACTIVATOR P52/P75. [RefSeq;Acc:NM_033222]
0.163477 SRD5A1 0.0411277 1091 0.251580956 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]
0.163636 no value 0.0436424 672 0.266704148
0.163681 HIVEP2 0.0401322 1349 0.245185452 HUMAN IMMUNODEFICIENCY VIRUS TYPE I ENHANCER-BINDING PROTEIN 2 (HIV-EP2). [SWISSPROT;Acc:P31629]
0.163741 no value 0.038359 1823 0.234266311
ANK2 1824 "ANKYRIN 2 (BRAIN ANKYRIN) (ANKYRIN B) (ANKYRIN, NONERYTHROID). [SWISSPROT;Acc:Q01484]"
ARL3 1822 ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 3. [SWISSPROT;Acc:P36405]
0.163819 BRP44 0.0199967 3010 0.122065817 BRAIN PROTEIN 44. [SWISSPROT;Acc:O95563]
0.163824 no value 0.0394801 1567 0.240990941 NEFA-INTERACTING NUCLEAR PROTEIN NIP30. [RefSeq;Acc:NM_024946]
ARL1 1566 ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 1. [SWISSPROT;Acc:P40616]
0.164816 CFL1 0.0460179 370 0.279207723 "COFILIN, NON-MUSCLE ISOFORM (18 KDA PHOSPHOPROTEIN) (P18). [SWISSPROT;Acc:P23528]"

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/