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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measured Rank Hugo Gene expected description final
Results: HTML CSV LaTeX Showing element 1351 to 1400 of 3206 in total
measured
Rank
Hugo
expected
description
final
0.0943614 942 C1orf121 0.368015 0.256406396
0.0943663 2688 EHD4 0.453066 EH-DOMAIN CONTAINING PROTEIN 4 (EH DOMAIN-CONTAINING PROTEIN FKSG7) (HEPATOCELLULAR CARCINOMA-ASSOCIATED PROTEIN 10/11). [SWISSPROT;Acc:Q9H223] 0.208283782
0.0944765 1455 ATP2C1 0.388558 "CALCIUM-TRANSPORTING ATPASE TYPE 2C, MEMBER 1 (EC 3.6.3.8) (ATPASE 2C1) (ATP-DEPENDENT CA(2+) PUMP PMR1) (HUSSY-28). [SWISSPROT;Acc:P98194]" 0.243146454
0.094576 1737 QRSL1 0.399107 GLUTAMINYL-TRNA SYNTHASE (GLUTAMINE-HYDROLYZING)-LIKE 1. [RefSeq;Acc:NM_018292] 0.236969033
0.0946162 1574 MACF1 0.392702 "MICROTUBULE-ACTIN CROSSLINKING FACTOR 1, ISOFORM 4. [SWISSPROT;Acc:Q96PK2]" 0.240936384
0.0946163 1370 no value 0.386406 HISTONE H2B.S (H2B/S). [SWISSPROT;Acc:P57053] 0.244862399
0.0946707 1739 UNG 0.399507 "URACIL-DNA GLYCOSYLASE, MITOCHONDRIAL PRECURSOR (EC 3.2.2.-) (UDG). [SWISSPROT;Acc:P13051]" 0.236968814
1740 PET112L "PROBABLE GLUTAMYL-TRNA(GLN) AMIDOTRANSFERASE SUBUNIT B, MITOCHONDRIAL PRECURSOR (EC 6.3.5.-) (GLU-ADT SUBUNIT B) (CYTOCHROME OXIDASE ASSEMBLY FACTOR PET112 HOMOLOG). [SWISSPROT;Acc:O75879]"
0.0946713 328 PRDX4 0.331704 PEROXIREDOXIN 4 (EC 1.11.1.-) (PRX-IV) (THIOREDOXIN PEROXIDASE AO372) (THIOREDOXIN-DEPENDENT PEROXIDE REDUCTASE A0372) (ANTIOXIDANT ENZYME AOE372) (AOE37-2). [SWISSPROT;Acc:Q13162] 0.285408979
0.0947181 1738 FAAH 0.399707 FATTY-ACID AMIDE HYDROLASE (EC 3.1.-.-) (OLEAMIDE HYDROLASE) (ANANDAMIDE AMIDOHYDROLASE). [SWISSPROT;Acc:O00519] 0.23696883
0.0948257 582 no value 0.351165 "SERINE/THREONINE PROTEIN PHOSPHATASE 2A, 55 KDA REGULATORY SUBUNIT B, ALPHA ISOFORM (PP2A, SUBUNIT B, B-ALPHA ISOFORM) (PP2A, SUBUNIT B, B55-ALPHA ISOFORM) (PP2A, SUBUNIT B, PR55-ALPHA ISOFORM) (PP2A, SUBUNIT B, R2-ALPHA ISOFORM). [SWISSPROT;Acc:Q0" 0.270031751
0.0949008 2811 RPP25 0.481532 0.197080983
0.0949294 2805 ZBTB7B 0.480144 KRUPPEL-RELATED ZINC FINGER PROTEIN HCKROX. [RefSeq;Acc:NM_015872] 0.19771027
0.095104 975 SON 0.372361 SON PROTEIN (SON3) (NEGATIVE REGULATORY ELEMENT-BINDING PROTEIN) (NRE- BINDING PROTEIN) (DBP-5) (BAX ANTAGONIST SELECTED IN SACCHAROMYCES 1) (BASS1) (PROTEIN C21ORF50). [SWISSPROT;Acc:P18583] 0.255408058
0.0951162 583 PPP2R2D 0.352242 UNCHARACTERIZED HEMATOPOIETIC STEM/PROGENITOR CELLS PROTEIN MDS026. [SPTREMBL;Acc:Q9NZ48] 0.270030831
0.0954445 26 DOK2 0.223986 DOCKING PROTEIN 2 (P56(DOK-2)) (DOWNSTREAM OF TYROSINE KINASE 2). [SWISSPROT;Acc:O60496] 0.42611815
0.0954996 629 CYP4X1 0.355998 LIKELY ORTHOLOG OF RAT CYTOCHROME P450 4X1. [RefSeq;Acc:NM_178033] 0.26825881
0.0956601 196 MXD4 0.296607 MAX-INTERACTING TRANSCRIPTIONAL REPRESSOR MAD4 (MAX-ASSOCIATED PROTEIN 4) (MAX DIMERIZATION PROTEIN 4). [SWISSPROT;Acc:Q14582] 0.322514641
0.0957148 1365 no value 0.390892 HISTONE H2B.D (H2B/D). [SWISSPROT;Acc:Q99877] 0.24486252
0.0957295 2759 SAPS3 0.472418 SPORULATION-INDUCED TRANSCRIPT 4-ASSOCIATED PROTEIN. [RefSeq;Acc:NM_018312] 0.202637283
0.0957789 1017 HRB 0.377297 NUCLEOPORIN-LIKE PROTEIN RIP (HIV-1 REV-BINDING PROTEIN) (REV INTERACTING PROTEIN) (REV/REX ACTIVATION DOMAIN-BINDING PROTEIN). [SWISSPROT;Acc:P52594] 0.253855451
0.0958474 608 LANCL2 0.356373 LANC LANTIBIOTIC SYNTHETASE COMPONENT C-LIKE 2; TESTIS-SPECIFIC ADRIAMYCIN SENSITIVITY PROTEIN; LANC (BACTERIAL LANTIBIOTIC SYNTHETASE COMPONENT C)-LIKE 2; G PROTEIN-COUPLED RECEPTOR 69B. [RefSeq;Acc:NM_018697] 0.268952474
0.0958705 1661 ATP7B 0.401402 COPPER-TRANSPORTING ATPASE 2 (EC 3.6.3.4) (COPPER PUMP 2) (WILSON DISEASE-ASSOCIATED PROTEIN). [SWISSPROT;Acc:P35670] 0.238839119
0.0959848 1138 TYRL 0.383295 "TYROSINASE-RELATED GENE SEGMENT, EXON 5 (FRAGMENT). [SPTREMBL;Acc:Q15677]" 0.250420172
0.0960386 627 CYP4B1 0.358007 CYTOCHROME P450 4B1 (EC 1.14.14.1) (CYPIVB1) (P450-HP). [SWISSPROT;Acc:P13584] 0.268259001
0.0960725 1369 HIST2H2BA 0.392353 HISTONE H2B.Q (H2B/Q) (H2B-GL105). [SWISSPROT;Acc:Q16778] 0.244862407
0.0961987 584 PPP2R2B 0.356254 "SERINE/THREONINE PROTEIN PHOSPHATASE 2A, 55 KDA REGULATORY SUBUNIT B, BETA ISOFORM (PP2A, SUBUNIT B, B-BETA ISOFORM) (PP2A, SUBUNIT B, B55- BETA ISOFORM) (PP2A, SUBUNIT B, PR55-BETA ISOFORM) (PP2A, SUBUNIT B, R2-BETA ISOFORM). [SWISSPROT;Acc:Q00005" 0.270028407
0.0962556 891 PRR5 0.370389 RHO-GTPASE-ACTIVATING PROTEIN 8. [SWISSPROT;Acc:Q9NSG0] 0.259877048
0.0963108 332 NDUFS8 0.337743 "NADH-UBIQUINONE OXIDOREDUCTASE 23 KDA SUBUNIT, MITOCHONDRIAL PRECURSOR (EC 1.6.5.3) (EC 1.6.99.3) (COMPLEX I-23KD) (CI-23KD) (TYKY SUBUNIT). [SWISSPROT;Acc:O00217]" 0.285160018
0.0963713 2606 HMGCR 0.454692 3-HYDROXY-3-METHYLGLUTARYL-COENZYME A REDUCTASE (EC 1.1.1.34) (HMG-COA REDUCTASE). [SWISSPROT;Acc:P04035] 0.211948528
0.096416 158 NEURL 0.274876 NEURALIZED-LIKE. [RefSeq;Acc:NM_004210] 0.350761798
0.0966308 2201 CYB5R3 0.427993 NADH-CYTOCHROME B5 REDUCTASE (EC 1.6.2.2) (B5R). [SWISSPROT;Acc:P00387] 0.22577659
0.0966625 2081 C6orf153 0.421972 0.229073256
0.0967095 2729 GPT 0.470166 ALANINE AMINOTRANSFERASE (EC 2.6.1.2) (GLUTAMIC--PYRUVIC TRANSAMINASE) (GPT) (GLUTAMIC--ALANINE TRANSAMINASE). [SWISSPROT;Acc:P24298] 0.205692245
0.0967911 1706 ACTR1A 0.407134 ALPHA-CENTRACTIN (CENTRACTIN) (CENTROSOME-ASSOCIATED ACTIN HOMOLOG) (ACTIN-RPV) (ARP1). [SWISSPROT;Acc:P42024] 0.237737698
0.0968147 509 SNUPN 0.353554 "RNA, U TRANSPORTER 1; SNURPORTIN-1. [RefSeq;Acc:NM_005701]" 0.273832852
0.0973611 1748 GDAP1 0.411298 GANGLIOSIDE-INDUCED DIFFERENTIATION-ASSOCIATED PROTEIN 1. [RefSeq;Acc:NM_018972] 0.236716687
0.0974156 1923 SLC35B1 0.419969 "SOLUTE CARRIER FAMILY 35, MEMBER B1; UDP-GALACTOSE TRANSPORTER RELATED. [RefSeq;Acc:NM_005827]" 0.231959026
0.0975531 1300 BAG3 0.396904 BAG-FAMILY MOLECULAR CHAPERONE REGULATOR-3 (BCL-2 BINDING ATHANOGENE- 3) (BAG-3) (BCL-2-BINDING PROTEIN BIS) (DOCKING PROTEIN CAIR-1). [SWISSPROT;Acc:O95817] 0.245785127
0.097609 2196 TP53BP2 0.431998 TUMOR SUPPRESSOR P53-BINDING PROTEIN 2 (P53-BINDING PROTEIN 2) (53BP2) (BCL2-BINDING PROTEIN) (BBP). [SWISSPROT;Acc:Q13625] 0.225947805
0.0978055 675 NSFL1C 0.367477 P47 PROTEIN ISOFORM A. [RefSeq;Acc:NM_016143] 0.266154072
0.0979343 783 WBP2 0.372839 WW DOMAIN BINDING PROTEIN 2 (WBP-2). [SWISSPROT;Acc:Q969T9] 0.262671823
0.0979655 3084 GNB3 0.982529 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(T) BETA SUBUNIT 3 (TRANSDUCIN BETA CHAIN 3). [SWISSPROT;Acc:P16520] 0.09970749
0.0979801 2079 no value 0.427723 LIM DOMAIN BINDING 1; CARBOXY TERMINAL LIM DOMAIN PROTEIN 2; LIM DOMAIN-BINDING FACTOR-1. [RefSeq;Acc:NM_003893] 0.229073723
0.0979873 1024 0.386626 UBIQUITIN-LIKE PROTEIN SMT3B (SENTRIN 2) (HSMT3). [SWISSPROT;Acc:P55855] 0.253442086
0.0982055 1285 GPR158 0.399189 0.24601254
0.098396 2432 THNSL1 0.452567 0.217417532
0.0985042 223 XPR1 0.309963 XENOTROPIC AND POLYTROPIC RETROVIRUS RECEPTOR. [RefSeq;Acc:NM_004736] 0.317793414
0.0986496 1792 DHDH 0.419992 DIMERIC DIHYDRODIOL DEHYDROGENASE; 3-DEOXYGLUCOSONE REDUCTASE. [RefSeq;Acc:NM_014475] 0.234884474
0.098654 2207 SLC47A2 0.437657 0.225413966

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/