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

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/