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.


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description Rank Gene Hugo expected measured final
Results: HTML CSV LaTeX Showing element 601 to 650 of 3206 in total
description
Rank
Hugo
expected
measured
final
"DELTA3,5-DELTA2,4-DIENOYL-COA ISOMERASE, MITOCHONDRIAL PRECURSOR (EC 5.3.3.-). [SWISSPROT;Acc:Q13011]" 72 ECH1 0.770597 0.31296 0.406126678
"DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE, MITOCHONDRIAL PRECURSOR (EC 3.6.1.23) (DUTPASE) (DUTP PYROPHOSPHATASE). [SWISSPROT;Acc:P33316]" 2884 DUT 0.860412 0.158579 0.184305891
"DIHYDROLIPOAMIDE ACETYLTRANSFERASE COMPONENT OF PYRUVATE DEHYDROGENASE COMPLEX, MITOCHONDRIAL PRECURSOR (EC 2.3.1.12) (E2) (PDC-E2) (70 KDA MITOCHONDRIAL AUTOANTIGEN OF PRIMARY BILIARY CIRRHOSIS) (PBC) (M2 ANTIGEN COMPLEX 70 KDA SUBUNIT). [SWISSPRO" 2194 DLAT 2.68753 0.607431 0.226018314
"DIHYDROLIPOAMIDE DEHYDROGENASE, MITOCHONDRIAL PRECURSOR (EC 1.8.1.4) (GLYCINE CLEAVAGE SYSTEM L PROTEIN). [SWISSPROT;Acc:P09622]" 1774 DLD 2.52689 0.596138 0.23591767
"DIHYDROLIPOAMIDE SUCCINYLTRANSFERASE COMPONENT OF 2-OXOGLUTARATE DEHYDROGENASE COMPLEX, MITOCHONDRIAL PRECURSOR (EC 2.3.1.61) (E2) (E2K). [SWISSPROT;Acc:P36957]" 1768 DLSTP 2.79908 0.660595 0.23600433
"DIHYDROOROTATE DEHYDROGENASE, MITOCHONDRIAL PRECURSOR (EC 1.3.3.1) (DIHYDROOROTATE OXIDASE) (DHODEHASE) (FRAGMENT). [SWISSPROT;Acc:Q02127]" 2269 DHODH 1.41191 0.314489 0.222740118
"DJ18D14.4 (CYTOCHROME P450, SUBFAMILY IVA, POLYPEPTIDE 11). [SPTREMBL;Acc:Q9NTL5]" 636 CYP4A22 0.432472 0.116014 0.268257829
"DJ681N20.2 (NOVEL PROTEIN SIMILAR TO FERRITIN, LIGHT POLYPEPTIDE (FTL)). [SPTREMBL;Acc:Q9BYW6]" 58 no value 0.124441 0.0511645 0.411154684
"DJ850E9.1 (NOVEL C2H2 TYPE ZINC FINGER PROTEIN SIMILAR TO DROSOPHILA SCRATCH (SCRT), SLUG AND XENOPUS SNAIL) (FRAGMENT). [SPTREMBL;Acc:Q9NQ03]" 1766 1.1936 0.281698 0.236007038
"DNA POLYMERASE EPSILON, CATALYTIC SUBUNIT A (EC 2.7.7.7) (DNA POLYMERASE II SUBUNIT A). [SWISSPROT;Acc:Q07864]" 235 POLE 0.824492 0.259541 0.314788985
"DNA TOPOISOMERASE II, ALPHA ISOZYME (EC 5.99.1.3). [SWISSPROT;Acc:P11388]" 2552 no value 1.33628 0.286606 0.214480498
"DNA TOPOISOMERASE II, BETA ISOZYME (EC 5.99.1.3). [SWISSPROT;Acc:Q02880]" 2554 TOP2B 1.16185 0.249175 0.214464001
"DNA-DIRECTED RNA POLYMERASES I, II, AND III 17.1 KDA POLYPEPTIDE (EC 2.7.7.6) (RPB17) (RPB8) (RPABC3). [SWISSPROT;Acc:P52434]" 1541 POLR2H 1.42971 0.345751 0.241832959
"DYNEIN INTERMEDIATE CHAIN 1, CYTOSOLIC (DH IC-1) (CYTOPLASMIC DYNEIN INTERMEDIATE CHAIN 1). [SWISSPROT;Acc:O14576]" 385 DYNC1I1 0.373698 0.104222 0.278893652
"DYNEIN INTERMEDIATE CHAIN 2, CYTOSOLIC (DH IC-2) (CYTOPLASMIC DYNEIN INTERMEDIATE CHAIN 2). [SWISSPROT;Acc:Q13409]" 375 DYNC1I2 0.428154 0.119541 0.279200942
"EARLY ENDOSOME ANTIGEN 1, 162KD; EARLY ENDOSOME-ASSOCIATED PROTEIN. [RefSeq;Acc:NM_003566]" 1807 EEA1 0.165025 0.0387072 0.234553552
"EGF-LIKE-DOMAIN, MULTIPLE 7; NEU1 PROTEIN. [RefSeq;Acc:NM_016215]" 3124 EGFL7 1.55221 0.117485 0.075688857
"ELECTRON TRANSFER FLAVOPROTEIN ALPHA-SUBUNIT, MITOCHONDRIAL PRECURSOR (ALPHA-ETF). [SWISSPROT;Acc:P13804]" 2778 ETFA 1.97038 0.396527 0.201243922
"ELECTRON TRANSFER FLAVOPROTEIN-UBIQUINONE OXIDOREDUCTASE, MITOCHONDRIAL PRECURSOR (EC 1.5.5.1) (ETF-QO) (ETF-UBIQUINONE OXIDOREDUCTASE) (ETF DEHYDROGENASE) (ELECTRON-TRANSFERRING- FLAVOPROTEIN DEHYDROGENASE). [SWISSPROT;Acc:Q16134]" 2662 ETFDH 0.548489 0.114957 0.209588524
"ENDONUCLEASE G, MITOCHONDRIAL PRECURSOR (EC 3.1.30.-) (ENDO G). [SWISSPROT;Acc:Q14249]" 2696 ENDOG 0.19727 0.0410294 0.207986009
"ENOYL-COA HYDRATASE, MITOCHONDRIAL PRECURSOR (EC 4.2.1.17) (SHORT CHAIN ENOYL-COA HYDRATASE) (SCEH) (ENOYL-COA HYDRATASE 1). [SWISSPROT;Acc:P30084]" 2874 ECHS1 0.643957 0.121508 0.188689617
"EUKARYOTIC TRANSLATION INITIATION FACTOR 4 GAMMA, 3. [RefSeq;Acc:NM_003760]" 259 EIF4G3 2.7378 0.84511 0.308682154
"EXONUCLEASE 1 ISOFORM B; RAD2 NUCLEASE FAMILY MEMBER, HOMOLOG OF S. CEREVISIAE EXONUCLEASE 1. [RefSeq;Acc:NM_006027]" 1076 EXO1 0.151786 0.03829 0.252263055
"EXPORTIN 1; EXPORTIN-1 (REQUIRED FOR CHROMOSOME REGION MAINTENANCE); EXPORTIN 1 (CRM1, YEAST, HOMOLOG); CRM1, YEAST, HOMOLOG. [RefSeq;Acc:NM_003400]" 2615 XPO1 0.75356 0.159172 0.211226711
"F-BOX PROTEIN FBW7 ISOFORM 2; ARCHIPELAGO, DROSOPHILA, HOMOLOG OF; F-BOX PROTEIN FBW7; F-BOX PROTEIN SEL-10; HOMOLOG OF C ELEGANS SEL-10. [RefSeq;Acc:NM_018315]" 3182 FBXW7 1.77573 0.0883895 0.04977643
"FATTY ACID-BINDING PROTEIN, ADIPOCYTE (AFABP) (ADIPOCYTE LIPID-BINDING PROTEIN) (ALBP) (A-FABP). [SWISSPROT;Acc:P15090]" 292 FABP4 0.12452 0.0375812 0.301808545
"FATTY ACID-BINDING PROTEIN, BRAIN (B-FABP) (BRAIN LIPID-BINDING PROTEIN) (BLBP) (MAMMARY DERIVED GROWTH INHIBITOR RELATED). [SWISSPROT;Acc:O15540]" 282 FABP7 0.127753 0.0385572 0.301810525
"FATTY ACID-BINDING PROTEIN, EPIDERMAL (E-FABP) (PSORIASIS-ASSOCIATED FATTY ACID-BINDING PROTEIN HOMOLOG) (PA-FABP). [SWISSPROT;Acc:Q01469]" 287 no value 0.110947 0.0334849 0.301809873
"FATTY ACID-BINDING PROTEIN, HEART (H-FABP) (MUSCLE FATTY ACID-BINDING PROTEIN) (M-FABP) (MAMMARY-DERIVED GROWTH INHIBITOR) (MDGI). [SWISSPROT;Acc:P05413]" 286 FABP3 0.153258 0.0462548 0.30181002
"FILAMIN B, BETA (ACTIN BINDING PROTEIN 278); BETA FILAMIN; FILAMIN 1 (ACTIN-BINDING PROTEIN-280)-LIKE; FILAMIN B, BETA (ACTIN-BINDING PROTEIN-278); FILAMIN B, BETA. [RefSeq;Acc:NM_001457]" 179 FLNB 0.111754 0.0376993 0.33734184
"FOLYLPOLYGLUTAMATE SYNTHASE, MITOCHONDRIAL PRECURSOR (EC 6.3.2.17) (FOLYLPOLY-GAMMA-GLUTAMATE SYNTHETASE) (FPGS). [SWISSPROT;Acc:Q05932]" 1798 FPGS 0.457652 0.107427 0.234735126
"FRUCTOSE-1,6-BISPHOSPHATASE (EC 3.1.3.11) (D-FRUCTOSE-1,6-BISPHOSPHATE 1-PHOSPHOHYDROLASE) (FBPASE). [SWISSPROT;Acc:P09467]" 979 FBP1 0.535042 0.136601 0.255308929
"FRUCTOSE-1,6-BISPHOSPHATASE ISOZYME 2 (EC 3.1.3.11) (D-FRUCTOSE-1,6- BISPHOSPHATE 1-PHOSPHOHYDROLASE) (FBPASE). [SWISSPROT;Acc:O00757]" 983 FBP2 0.47704 0.12174 0.255198725
"FTSJ HOMOLOG 3; LIKELY ORTHOLOG OF MOUSE ECTOPLACENTAL CONE, INVASIVE TROPHOBLAST GIANT CELLS, EXTRAEMBRYONIC ECTODERM AND CHORION SEQUENCE 3. [RefSeq;Acc:NM_017647]" 1021 FTSJ3 1.10792 0.280943 0.253576973
"FUMARATE HYDRATASE, MITOCHONDRIAL PRECURSOR (EC 4.2.1.2) (FUMARASE). [SWISSPROT;Acc:P07954]" 1002 FH 0.51515 0.131317 0.25491022
"GAMMA-BUTYROBETAINE,2-OXOGLUTARATE DIOXYGENASE (EC 1.14.11.1) (GAMMA-BUTYROBETAINE HYDROXYLASE) (GAMMA-BBH). [SWISSPROT;Acc:O75936]" 1082 BBOX1 0.203883 0.0513934 0.252073003
"GAMMA-SOLUBLE NSF ATTACHMENT PROTEIN (SNAP-GAMMA) (N-ETHYLMALEIMIDE- SENSITIVE FACTOR ATTACHMENT PROTEIN, GAMMA). [SWISSPROT;Acc:Q99747]" 1729 NAPG 0.238547 0.056545 0.237039242
"GLUTAMATE DECARBOXYLASE, 65 KDA ISOFORM (EC 4.1.1.15) (GAD-65) (65 KDA GLUTAMIC ACID DECARBOXYLASE). [SWISSPROT;Acc:Q05329]" 1727 GAD2 0.0742417 0.0175982 0.237039292
"GLUTAMATE DECARBOXYLASE, 67 KDA ISOFORM (EC 4.1.1.15) (GAD-67) (67 KDA GLUTAMIC ACID DECARBOXYLASE). [SWISSPROT;Acc:Q99259]" 1732 GAD1 0.0899059 0.0213112 0.237038949
"GLUTAMATE DEHYDROGENASE 1, MITOCHONDRIAL PRECURSOR (EC 1.4.1.3) (GDH). [SWISSPROT;Acc:P00367]" 2087 GLUDP5 0.654219 0.149641 0.228732275
"GLUTAMATE DEHYDROGENASE 2, MITOCHONDRIAL PRECURSOR (EC 1.4.1.3) (GDH). [SWISSPROT;Acc:P49448]" 2086 GLUD2
"GLUTARYL-COA DEHYDROGENASE, MITOCHONDRIAL PRECURSOR (EC 1.3.99.7) (GCD). [SWISSPROT;Acc:Q92947]" 693 GCDH 0.472616 0.125547 0.265642721
"GLUTATHIONE REDUCTASE, MITOCHONDRIAL PRECURSOR (EC 1.8.1.7) (GR) (GRASE). [SWISSPROT;Acc:P00390]" 2098 GSR 1.98642 0.453634 0.228367616
"GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE, LIVER (EC 1.2.1.12) (GAPDH). [SWISSPROT;Acc:P04406]" 1689 GAPDH 1.74133 0.414602 0.238095019
"GLYCEROL KINASE, TESTIS SPECIFIC 1 (EC 2.7.1.30) (ATP:GLYCEROL 3- PHOSPHOTRANSFERASE) (GLYCEROKINASE) (GK). [SWISSPROT;Acc:Q14409]" 2272 no value 0.591632 0.131767 0.222717838
"GLYCEROL KINASE, TESTIS SPECIFIC 2 (EC 2.7.1.30) (ATP:GLYCEROL 3- PHOSPHOTRANSFERASE) (GLYCEROKINASE) (GK). [SWISSPROT;Acc:Q14410]" 2273 0.615573 0.137099 0.222717696
"GLYCEROL-3-PHOSPHATE DEHYDROGENASE [NAD+], CYTOPLASMIC (EC 1.1.1.8) (GPD-C) (GPDH-C). [SWISSPROT;Acc:P21695]" 2061 GPD1 0.674093 0.1548 0.229641904
"GLYCEROL-3-PHOSPHATE DEHYDROGENASE, MITOCHONDRIAL PRECURSOR (EC 1.1.99.5) (GPD-M) (GPDH-M). [SWISSPROT;Acc:P43304]" 2251 GPD2 0.50755 0.113261 0.223152399
"GLYCINE CLEAVAGE SYSTEM H PROTEIN, MITOCHONDRIAL PRECURSOR. [SWISSPROT;Acc:P23434]" 2180 no value 0.916816 0.207889 0.22675106
"GLYCINE DEHYDROGENASE [DECARBOXYLATING], MITOCHONDRIAL PRECURSOR (EC 1.4.4.2) (GLYCINE DECARBOXYLASE) (GLYCINE CLEAVAGE SYSTEM P- PROTEIN). [SWISSPROT;Acc:P23378]" 2127 0.280704 0.0640341 0.228119656

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/