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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Rank Gene expected description measured Hugo final
Results: HTML CSV LaTeX Showing element 1001 to 1050 of 3206 in total
Rank
expected
description
measured
Hugo
final
1001 0.262934 MITOCHONDRIAL IMPORT INNER MEMBRANE TRANSLOCASE SUBUNIT TIM10. [SWISSPROT;Acc:Q9Y5J8] 0.0670247 TIMM10 0.254910738
1002 0.51515 "FUMARATE HYDRATASE, MITOCHONDRIAL PRECURSOR (EC 4.2.1.2) (FUMARASE). [SWISSPROT;Acc:P07954]" 0.131317 FH 0.25491022
1003 0.110551 HUNTINGTIN INTERACTING PROTEIN E; HUNTINGTIN INTERACTOR PROTEIN E. [RefSeq;Acc:NM_007076] 0.0281805 no value 0.254909499
1004 0.54802 PROBABLE SERINE/THREONINE-PROTEIN KINASE KIAA0537 (EC 2.7.1.-). [SWISSPROT;Acc:O60285] 0.139695 NUAK1 0.25490858
1005 0.542366 DEOXYHYPUSINE SYNTHASE (EC 2.5.1.46) (DHS). [SWISSPROT;Acc:P49366] 0.138205 DHPS 0.254818702
1006 0.831867 ORPHAN NUCLEAR RECEPTOR TR2. [SWISSPROT;Acc:P13056] 0.211877 NR2C1 0.254700571
1007 1.10266 ORPHAN NUCLEAR RECEPTOR NR2E1 (NUCLEAR RECEPTOR TLX) (TAILLESS HOMOLOG) (TLL) (HTLL). [SWISSPROT;Acc:Q9Y466] 0.280845 NR2E1 0.254697731
1008 0.897587 TRAF AND TNF RECEPTOR-ASSOCIATED PROTEIN; ETS1-ASSOCIATED PROTEIN 2. [RefSeq;Acc:NM_016614] 0.228495 TTRAP 0.254565853
1009 0.162467 0.0413585 C20orf72 0.254565543
1010 0.87407 PUTATATIVE 28 KDA PROTEIN. [RefSeq;Acc:NM_020143] 0.222495 PNO1 0.254550551
1011 1.24807 SORTING NEXIN 5. [SWISSPROT;Acc:Q9Y5X3] 0.317621 SNX5 0.254489732
1012 0.495862 BETA-CATENIN (PRO2286). [SWISSPROT;Acc:P35222] 0.126011 CTNNB1 0.25412514
1013 1.35164 TRANSCRIPTION INITIATION FACTOR TFIID 28 KDA SUBUNIT (TAFII-28) (TAFII28) (TFIID SUBUNIT P30-BETA). [SWISSPROT;Acc:Q15544] 0.343318 TAF11 0.254001065
1014 0.290228 HIV-1 REV BINDING PROTEIN-LIKE; REV/REX ACTIVATION DOMAIN BINDING PROTEIN-RELATED. [RefSeq;Acc:NM_006076] 0.0736761 HRBL 0.253855934
1015 0.314025 INTERSECTIN 2 (SH3 DOMAIN-CONTAINING PROTEIN 1B) (SH3P18) (SH3P18-LIKE WASP ASSOCIATED PROTEIN). [SWISSPROT;Acc:Q9NZM3] 0.079717 no value 0.253855585
1016 0.91233 PRAM-1 PROTEIN; PML-RARA TARGET GENE ENCODING AN ADAPTOR MOLECULE-1. [RefSeq;Acc:NM_032152] 0.2316 PRAM1 0.253855513
1017 0.377297 NUCLEOPORIN-LIKE PROTEIN RIP (HIV-1 REV-BINDING PROTEIN) (REV INTERACTING PROTEIN) (REV/REX ACTIVATION DOMAIN-BINDING PROTEIN). [SWISSPROT;Acc:P52594] 0.0957789 HRB 0.253855451
1018 0.233925 CGTHBA PROTEIN (-14 GENE PROTEIN). [SWISSPROT;Acc:Q12980] 0.0593831 C16orf35 0.253855296
1019 0.365399 INTERSECTIN 1 (SH3 DOMAIN-CONTAINING PROTEIN 1A) (SH3P17). [SWISSPROT;Acc:Q15811] 0.0927584 no value 0.253855101
1020 0.131474 HIV TAT SPECIFIC FACTOR 1; COFACTOR REQUIRED FOR TAT ACTIVATION OF HIV-1 TRANSCRIPTION. [RefSeq;Acc:NM_014500] 0.0333753 HTATSF1 0.253854755
1021 1.10792 "FTSJ HOMOLOG 3; LIKELY ORTHOLOG OF MOUSE ECTOPLACENTAL CONE, INVASIVE TROPHOBLAST GIANT CELLS, EXTRAEMBRYONIC ECTODERM AND CHORION SEQUENCE 3. [RefSeq;Acc:NM_017647]" 0.280943 FTSJ3 0.253576973
1022 0.705791 0.178897 TBC1D10B 0.25347022
1023 0.731277 SHORT TRANSIENT RECEPTOR POTENTIAL CHANNEL 4 (TRPC4) (TRP-RELATED PROTEIN 4) (HTRP-4) (HTRP4). [SWISSPROT;Acc:Q9UBN4] 0.185352 TRPC4 0.253463462
1024 0.386626 UBIQUITIN-LIKE PROTEIN SMT3B (SENTRIN 2) (HSMT3). [SWISSPROT;Acc:P55855] 0.0979873 no value 0.253442086
1025 0.256212 ACRC PROTEIN; PUTATIVE NUCLEAR PROTEIN. [RefSeq;Acc:NM_052957] 0.0649343 ACRC 0.25343973
1026 0.854644 SHORT TRANSIENT RECEPTOR POTENTIAL CHANNEL 5 (TRPC5) (HTRP-5) (HTRP5). [SWISSPROT;Acc:Q9UL62] 0.2166 TRPC5 0.253438859
1027 EBP50-PDZ INTERACTOR OF 64 KDA (EPI64 PROTEIN). [SWISSPROT;Acc:Q9BXI6] TBC1D10A
1028 0.401325 UBIQUITIN-LIKE PROTEIN SMT3A. [SWISSPROT;Acc:P55854] 0.101711 SUMO3 0.253437987
1029 1.11593 RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE M2 CHAIN (EC 1.17.4.1) (RIBONUCLEOTIDE REDUCTASE SMALL CHAIN). [SWISSPROT;Acc:P31350] 0.282811 RRM2 0.253430771
1030 0.600397 RETINOBLASTOMA-LIKE PROTEIN 2 (130 KDA RETINOBLASTOMA-ASSOCIATED PROTEIN) (PRB2) (P130) (RBR-2). [SWISSPROT;Acc:Q08999] 0.152107 RBL2 0.253344037
1031 0.250657 SODIUM/POTASSIUM-TRANSPORTING ATPASE ALPHA-2 CHAIN PRECURSOR (EC 3.6.3.9) (SODIUM PUMP 2) (NA+/K+ ATPASE 2). [SWISSPROT;Acc:P50993] 0.063502 ATP1A2 0.253342217
1032 SODIUM/POTASSIUM-TRANSPORTING ATPASE ALPHA-1 CHAIN PRECURSOR (EC 3.6.3.9) (SODIUM PUMP 1) (NA+/K+ ATPASE 1). [SWISSPROT;Acc:P05023] ATP1A1
1033 0.729445 CATHEPSIN L PRECURSOR (EC 3.4.22.15) (MAJOR EXCRETED PROTEIN) (MEP). [SWISSPROT;Acc:P07711] 0.184799 CTSL1 0.253341924
1034 0.290389 SODIUM/POTASSIUM-TRANSPORTING ATPASE ALPHA-3 CHAIN (EC 3.6.3.9) (SODIUM PUMP 3) (NA+/K+ ATPASE 3) (ALPHA(III)). [SWISSPROT;Acc:P13637] 0.0735677 ATP1A3 0.253341897
1035 0.646587 CATHEPSIN L2 PRECURSOR (EC 3.4.22.43) (CATHEPSIN V) (CATHEPSIN U). [SWISSPROT;Acc:O60911] 0.163807 CTSL2 0.253341004
1036 0.145611 UNR PROTEIN. [SWISSPROT;Acc:O75534] 0.0368889 CSDE1 0.25333869
1037 0.582446 LOH1CR12. [RefSeq;Acc:NM_058169] 0.147556 LOH12CR1 0.253338507
1038 0.506251 RETINOBLASTOMA-LIKE PROTEIN 1 (107 KDA RETINOBLASTOMA-ASSOCIATED PROTEIN) (PRB1) (P107). [SWISSPROT;Acc:P28749] 0.128252 RBL1 0.253336784
1039 1.34662 HEAT SHOCK PROTEIN HSP 90-BETA (HSP 84) (HSP 90). [SWISSPROT;Acc:P08238] 0.341129 HSP90AB1 0.253322392
1040 0.156754 "ATP-DEPENDENT DNA HELICASE II, 70 KDA SUBUNIT (LUPUS KU AUTOANTIGEN PROTEIN P70) (KU70) (70 KDA SUBUNIT OF KU ANTIGEN) (THYROID-LUPUS AUTOANTIGEN) (TLAA) (CTC BOX BINDING FACTOR 75 KDA SUBUNIT) (CTCBF) (CTC75). [SWISSPROT;Acc:P12956]" 0.0397033 no value 0.253284127
1041 0.294737 RAD17 HOMOLOG ISOFORM 1; RAD17-LIKE PROTEIN; CELL CYCLE CHECKPOINT PROTEIN (RAD17); RF-C ACTIVATOR 1 HOMOLOG. [RefSeq;Acc:NM_002873] 0.0746521 RAD17 0.253283775
1042 0.451492 "ATP-DEPENDENT DNA HELICASE II, 80 KDA SUBUNIT (LUPUS KU AUTOANTIGEN PROTEIN P86) (KU86) (KU80) (86 KDA SUBUNIT OF KU ANTIGEN) (THYROID- LUPUS AUTOANTIGEN) (TLAA) (CTC BOX BINDING FACTOR 85 KDA SUBUNIT) (CTCBF) (CTC85) (NUCLEAR FACTOR IV) (DNA-REPAIR PROTE" 0.114355 XRCC5 0.25328245
1043 0.12923 0.0327294 TMEM87B 0.253264722
1044 1.3576 0.343832 ASCC1 0.253264585
1045 0.168127 0.0425806 TMEM87A 0.253264496
1046 1.22676 HEAT SHOCK PROTEIN HSP 90-ALPHA (HSP 86). [SWISSPROT;Acc:P07900] 0.310662 HSP90AA2 0.253237797
1047 1.16068 SOLUBLE LIVER ANTIGEN/LIVER PANCREAS ANTIGEN. [RefSeq;Acc:NM_153825] 0.293391 SEPSECS 0.252775097
1048 0.451047 ANNEXIN A11 (ANNEXIN XI) (CALCYCLIN-ASSOCIATED ANNEXIN 50) (CAP-50) (56 KDA AUTOANTIGEN). [SWISSPROT;Acc:P50995] 0.114013 ANXA11 0.252774101
1049 0.14106 CALMEGIN PRECURSOR. [SWISSPROT;Acc:O14967] 0.0356563 CLGN 0.252773997
1050 0.169952 CALNEXIN PRECURSOR (MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I ANTIGEN-BINDING PROTEIN P88) (P90) (IP90). [SWISSPROT;Acc:P27824] 0.0429594 CANX 0.252773724

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/