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 description measured expected final Hugo
Results: HTML CSV LaTeX Showing element 1008 to 1057 of 3206 in total
Rank
description
measured
expected
final
Hugo
1008 TRAF AND TNF RECEPTOR-ASSOCIATED PROTEIN; ETS1-ASSOCIATED PROTEIN 2. [RefSeq;Acc:NM_016614] 0.228495 0.897587 0.254565853 TTRAP
1009 0.0413585 0.162467 0.254565543 C20orf72
1010 PUTATATIVE 28 KDA PROTEIN. [RefSeq;Acc:NM_020143] 0.222495 0.87407 0.254550551 PNO1
1011 SORTING NEXIN 5. [SWISSPROT;Acc:Q9Y5X3] 0.317621 1.24807 0.254489732 SNX5
1012 BETA-CATENIN (PRO2286). [SWISSPROT;Acc:P35222] 0.126011 0.495862 0.25412514 CTNNB1
1013 TRANSCRIPTION INITIATION FACTOR TFIID 28 KDA SUBUNIT (TAFII-28) (TAFII28) (TFIID SUBUNIT P30-BETA). [SWISSPROT;Acc:Q15544] 0.343318 1.35164 0.254001065 TAF11
1014 HIV-1 REV BINDING PROTEIN-LIKE; REV/REX ACTIVATION DOMAIN BINDING PROTEIN-RELATED. [RefSeq;Acc:NM_006076] 0.0736761 0.290228 0.253855934 HRBL
1015 INTERSECTIN 2 (SH3 DOMAIN-CONTAINING PROTEIN 1B) (SH3P18) (SH3P18-LIKE WASP ASSOCIATED PROTEIN). [SWISSPROT;Acc:Q9NZM3] 0.079717 0.314025 0.253855585 no value
1016 PRAM-1 PROTEIN; PML-RARA TARGET GENE ENCODING AN ADAPTOR MOLECULE-1. [RefSeq;Acc:NM_032152] 0.2316 0.91233 0.253855513 PRAM1
1017 NUCLEOPORIN-LIKE PROTEIN RIP (HIV-1 REV-BINDING PROTEIN) (REV INTERACTING PROTEIN) (REV/REX ACTIVATION DOMAIN-BINDING PROTEIN). [SWISSPROT;Acc:P52594] 0.0957789 0.377297 0.253855451 HRB
1018 CGTHBA PROTEIN (-14 GENE PROTEIN). [SWISSPROT;Acc:Q12980] 0.0593831 0.233925 0.253855296 C16orf35
1019 INTERSECTIN 1 (SH3 DOMAIN-CONTAINING PROTEIN 1A) (SH3P17). [SWISSPROT;Acc:Q15811] 0.0927584 0.365399 0.253855101 no value
1020 HIV TAT SPECIFIC FACTOR 1; COFACTOR REQUIRED FOR TAT ACTIVATION OF HIV-1 TRANSCRIPTION. [RefSeq;Acc:NM_014500] 0.0333753 0.131474 0.253854755 HTATSF1
1021 "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 1.10792 0.253576973 FTSJ3
1022 0.178897 0.705791 0.25347022 TBC1D10B
1023 SHORT TRANSIENT RECEPTOR POTENTIAL CHANNEL 4 (TRPC4) (TRP-RELATED PROTEIN 4) (HTRP-4) (HTRP4). [SWISSPROT;Acc:Q9UBN4] 0.185352 0.731277 0.253463462 TRPC4
1024 UBIQUITIN-LIKE PROTEIN SMT3B (SENTRIN 2) (HSMT3). [SWISSPROT;Acc:P55855] 0.0979873 0.386626 0.253442086 no value
1025 ACRC PROTEIN; PUTATIVE NUCLEAR PROTEIN. [RefSeq;Acc:NM_052957] 0.0649343 0.256212 0.25343973 ACRC
1026 SHORT TRANSIENT RECEPTOR POTENTIAL CHANNEL 5 (TRPC5) (HTRP-5) (HTRP5). [SWISSPROT;Acc:Q9UL62] 0.2166 0.854644 0.253438859 TRPC5
1027 EBP50-PDZ INTERACTOR OF 64 KDA (EPI64 PROTEIN). [SWISSPROT;Acc:Q9BXI6] TBC1D10A
1028 UBIQUITIN-LIKE PROTEIN SMT3A. [SWISSPROT;Acc:P55854] 0.101711 0.401325 0.253437987 SUMO3
1029 RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE M2 CHAIN (EC 1.17.4.1) (RIBONUCLEOTIDE REDUCTASE SMALL CHAIN). [SWISSPROT;Acc:P31350] 0.282811 1.11593 0.253430771 RRM2
1030 RETINOBLASTOMA-LIKE PROTEIN 2 (130 KDA RETINOBLASTOMA-ASSOCIATED PROTEIN) (PRB2) (P130) (RBR-2). [SWISSPROT;Acc:Q08999] 0.152107 0.600397 0.253344037 RBL2
1031 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 0.250657 0.253342217 ATP1A2
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 CATHEPSIN L PRECURSOR (EC 3.4.22.15) (MAJOR EXCRETED PROTEIN) (MEP). [SWISSPROT;Acc:P07711] 0.184799 0.729445 0.253341924 CTSL1
1034 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 0.290389 0.253341897 ATP1A3
1035 CATHEPSIN L2 PRECURSOR (EC 3.4.22.43) (CATHEPSIN V) (CATHEPSIN U). [SWISSPROT;Acc:O60911] 0.163807 0.646587 0.253341004 CTSL2
1036 UNR PROTEIN. [SWISSPROT;Acc:O75534] 0.0368889 0.145611 0.25333869 CSDE1
1037 LOH1CR12. [RefSeq;Acc:NM_058169] 0.147556 0.582446 0.253338507 LOH12CR1
1038 RETINOBLASTOMA-LIKE PROTEIN 1 (107 KDA RETINOBLASTOMA-ASSOCIATED PROTEIN) (PRB1) (P107). [SWISSPROT;Acc:P28749] 0.128252 0.506251 0.253336784 RBL1
1039 HEAT SHOCK PROTEIN HSP 90-BETA (HSP 84) (HSP 90). [SWISSPROT;Acc:P08238] 0.341129 1.34662 0.253322392 HSP90AB1
1040 "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 0.156754 0.253284127 no value
1041 RAD17 HOMOLOG ISOFORM 1; RAD17-LIKE PROTEIN; CELL CYCLE CHECKPOINT PROTEIN (RAD17); RF-C ACTIVATOR 1 HOMOLOG. [RefSeq;Acc:NM_002873] 0.0746521 0.294737 0.253283775 RAD17
1042 "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 0.451492 0.25328245 XRCC5
1043 0.0327294 0.12923 0.253264722 TMEM87B
1044 0.343832 1.3576 0.253264585 ASCC1
1045 0.0425806 0.168127 0.253264496 TMEM87A
1046 HEAT SHOCK PROTEIN HSP 90-ALPHA (HSP 86). [SWISSPROT;Acc:P07900] 0.310662 1.22676 0.253237797 HSP90AA2
1047 SOLUBLE LIVER ANTIGEN/LIVER PANCREAS ANTIGEN. [RefSeq;Acc:NM_153825] 0.293391 1.16068 0.252775097 SEPSECS
1048 ANNEXIN A11 (ANNEXIN XI) (CALCYCLIN-ASSOCIATED ANNEXIN 50) (CAP-50) (56 KDA AUTOANTIGEN). [SWISSPROT;Acc:P50995] 0.114013 0.451047 0.252774101 ANXA11
1049 CALMEGIN PRECURSOR. [SWISSPROT;Acc:O14967] 0.0356563 0.14106 0.252773997 CLGN
1050 CALNEXIN PRECURSOR (MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I ANTIGEN-BINDING PROTEIN P88) (P90) (IP90). [SWISSPROT;Acc:P27824] 0.0429594 0.169952 0.252773724 CANX
1051 RNA (GUANINE-7-) METHYLTRANSFERASE. [RefSeq;Acc:NM_003799] 0.0429379 0.169867 0.252773641 RNMT
1052 ANNEXIN A7 (ANNEXIN VII) (SYNEXIN). [SWISSPROT;Acc:P20073] 0.149169 0.590289 0.252705031 ANXA7
1053 CLATHRIN HEAVY CHAIN 1 (CLH-17). [SWISSPROT;Acc:Q00610] 0.264806 1.04802 0.252672659 CLTC
1054 PHOSDUCIN-LIKE PROTEIN (PHLP). [SWISSPROT;Acc:Q13371] 0.0344183 0.136218 0.252670719 PDCL
1055 DNA REPAIR PROTEIN RAD52 HOMOLOG. [SWISSPROT;Acc:P43351] RAD52
1056 REPLICATION PROTEIN A 70 KDA DNA-BINDING SUBUNIT (RP-A) (RF-A) (REPLICATION FACTOR-A PROTEIN 1) (SINGLE-STRANDED DNA-BINDING PROTEIN). [SWISSPROT;Acc:P27694] 0.0688366 0.272436 RPA1
1057 REPLICATION PROTEIN A 32 KDA SUBUNIT (RP-A) (RF-A) (REPLICATION FACTOR-A PROTEIN 2). [SWISSPROT;Acc:P15927] 0.160828 0.636513 0.252670409 RPA2

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/