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:
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expected description Hugo Rank final Gene measured
Results: HTML CSV LaTeX Showing element 501 to 550 of 3206 in total
expected
description
Hugo
Rank
final
measured
0.157329 no value 847 0.260622644 0.0410035
0.15771 "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 2101 0.228353307 0.0360136
"CYTOCHROME C OXIDASE SUBUNIT IV ISOFORM 2, MITOCHONDRIAL PRECURSOR (EC 1.9.3.1) (COX IV-2). [SWISSPROT;Acc:Q96KJ9]" COX4I2 2099
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 2100
0.157765 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 2622 0.209999683 0.0331306
0.158002 CENTAURIN GAMMA 1. [SWISSPROT;Acc:Q99490] CENTG1 402 0.278252807 0.0439645
0.158229 EXOCYST COMPLEX COMPONENT SEC6. [SWISSPROT;Acc:O60645] EXOC3 1509 0.24260281 0.0383868
0.158312 "SPECTRIN BETA CHAIN, BRAIN 1 (SPECTRIN, NON-ERYTHROID BETA CHAIN 1) (BETA-II SPECTRIN) (FODRIN BETA CHAIN). [SWISSPROT;Acc:Q01082]" SPTBN1 595 0.26932513 0.0426374
0.158511 RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 4 ISOFORM A; APC-STIMULATED GUANINE NUCLEOTIDE EXCHANGE FACTOR. [RefSeq;Acc:NM_015320] ARHGEF4 2091 0.228715357 0.0362539
0.158546 RNA HELICASE-RELATED PROTEIN; RNA HELICASE-LIKE PROTEIN; SF3B125 DEAD-BOX PROTEIN. [RefSeq;Acc:NM_007372] no value 1433 0.243657992 0.038631
0.159183 SPLICING COACTIVATOR SUBUNIT SRM300; RNA BINDING PROTEIN; AT-RICH ELEMENT BINDING FACTOR. [RefSeq;Acc:NM_016333] SRRM2 1435 0.2436573 0.0387861
0.159272 SETD3 2436 0.2172692 0.0346049
0.159275 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 68 0.406127139 0.0646859
0.15929 LRRC4C 543 0.27107728 0.0431799
0.159487 REST COREPRESSOR. [RefSeq;Acc:NM_015156] RCOR1 709 0.265146376 0.0422874
0.159562 LIMKAIN B1. [RefSeq;Acc:NM_019081] KIAA0430 51 0.411156165 0.0656049
0.159725 C20orf42 2511 0.214767256 0.0343037
0.159817 15 KDA SELENOPROTEIN PRECURSOR. [SWISSPROT;Acc:O60613] no value 698 0.265486775 0.0424293
0.159829 HUMAN IMMUNODEFICIENCY VIRUS TYPE I ENHANCER BINDING PROTEIN 3. [RefSeq;Acc:NM_024503] HIVEP3 1351 0.245185167 0.0391877
0.15995 PEROXISOMAL N1-ACETYL-SPERMINE/SPERMIDINE OXIDASE. [RefSeq;Acc:NM_152911] PAOX 443 0.276703345 0.0442587
0.160098 UPF0183 PROTEIN. [SWISSPROT;Acc:Q9BSU1] C16orf70 1578 0.240892453 0.0385664
0.160453 MAEA 1616 0.239635283 0.0384502
RMND5A 1617
0.160458 CHCHD4 1325 0.245522816 0.0393961
"28S RIBOSOMAL PROTEIN S26, MITOCHONDRIAL PRECURSOR (MRP-S26) (MRP- S13). [SWISSPROT;Acc:Q9BYN8]" MRPS26 1324
0.160664 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 2999 0.135091869 0.0217044
0.160934 SIN3B 2027 0.230298135 0.0370628
0.161679 GTP-BINDING PROTEIN ERA HOMOLOG (HERA) (FRAGMENT). [SWISSPROT;Acc:O75616] ERAL1 468 0.274905832 0.0444465
0.161745 "COP9 SUBUNIT 6 (MOV34 HOMOLOG, 34 KD). [RefSeq;Acc:NM_006833]" COPS6 1176 0.249396272 0.0403386
0.161954 MITOCHONDRIAL RIBOSOMAL PROTEIN L30 ISOFORM A. [RefSeq;Acc:NM_145212] MRPL30 1613 0.239731035 0.0388254
0.162108 "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 478 0.274304168 0.0444669
SHC TRANSFORMING PROTEIN. [SWISSPROT;Acc:P29353] SHC1 479
0.162467 C20orf72 1009 0.254565543 0.0413585
0.162737 ORAI1 2860 0.188941052 0.0307477
0.162874 FAM49B 18 0.475138451 0.0773877
0.16302 HISTONE DEACETYLASE 11 (HD11). [SWISSPROT;Acc:Q96DB2] HDAC11 1166 0.249397007 0.0406567
0.163123 BUD13 1295 0.245899107 0.0401118
SIMILAR TO ECOTROPIC VIRAL INTEGRATION SITE 5; NEUROBLASTOMA STAGE 4S GENE. [RefSeq;Acc:NM_145245] EVI5L 1296
0.163279 ORAI2 2867 0.188940403 0.03085
0.163476 PC4 AND SFRS1 INTERACTING PROTEIN 2; PC4 AND SFRS1 INTERACTING PROTEIN 1; TRANSCRIPTIONAL COACTIVATOR P52/P75. [RefSeq;Acc:NM_033222] PSIP1 2869 0.188940273 0.0308872
0.163477 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 1091 0.251580956 0.0411277
0.163636 no value 672 0.266704148 0.0436424
0.163681 HUMAN IMMUNODEFICIENCY VIRUS TYPE I ENHANCER-BINDING PROTEIN 2 (HIV-EP2). [SWISSPROT;Acc:P31629] HIVEP2 1349 0.245185452 0.0401322
0.163741 no value 1823 0.234266311 0.038359
"ANKYRIN 2 (BRAIN ANKYRIN) (ANKYRIN B) (ANKYRIN, NONERYTHROID). [SWISSPROT;Acc:Q01484]" ANK2 1824
ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 3. [SWISSPROT;Acc:P36405] ARL3 1822
0.163819 BRAIN PROTEIN 44. [SWISSPROT;Acc:O95563] BRP44 3010 0.122065817 0.0199967
0.163824 ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 1. [SWISSPROT;Acc:P40616] ARL1 1566 0.240990941 0.0394801
NEFA-INTERACTING NUCLEAR PROTEIN NIP30. [RefSeq;Acc:NM_024946] no value 1567
0.164816 "COFILIN, MUSCLE ISOFORM (COFILIN 2). [SWISSPROT;Acc:Q9Y281]" CFL2 372 0.279207723 0.0460179

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/