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

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/