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

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/