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