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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
measured Gene Rank description expected Hugo final
Results: HTML CSV LaTeX Showing element 551 to 600 of 3206 in total
measured
Rank
description
expected
Hugo
final
0.0385694 742 BARDET-BIEDL SYNDROME 7 PROTEIN ISOFORM A; BBS2-LIKE 1. [RefSeq;Acc:NM_176824] 0.145821 BBS7 0.264498255
743 HSDL2
0.0386201 1191 TATA BOX BINDING PROTEIN (TRANSCRIPTION INITIATION FACTOR TFIID) (TATA-BOX FACTOR) (TATA SEQUENCE-BINDING PROTEIN) (TBP). [SWISSPROT;Acc:P20226] 0.155349 TBP 0.24860218
1192 ATP13A4
0.0386224 2202 HEPARIN SULFATE N-DEACETYLASE/N-SULFOTRANSFERASE (EC 2.8.2.-) (N- HSST) (N-HEPARIN SULFATE SULFOTRANSFERASE) (GLUCOSAMINYL N- DEACETYLASE/N-SULFOTRANSFERASE). [SWISSPROT;Acc:P52849] 0.17129 NDST2 0.225479596
0.038631 1433 RNA HELICASE-RELATED PROTEIN; RNA HELICASE-LIKE PROTEIN; SF3B125 DEAD-BOX PROTEIN. [RefSeq;Acc:NM_007372] 0.158546 no value 0.243657992
0.038682 2125 0.169567 TCP11L1 0.228122217
0.0387072 1807 "EARLY ENDOSOME ANTIGEN 1, 162KD; EARLY ENDOSOME-ASSOCIATED PROTEIN. [RefSeq;Acc:NM_003566]" 0.165025 EEA1 0.234553552
0.0387137 1126 UBIQUITIN CARBOXYL-TERMINAL HYDROLASE ISOZYME L5 (EC 3.4.19.12) (UCH- L5) (UBIQUITIN THIOLESTERASE L5) (UBIQUITIN C-TERMINAL HYDROLASE UCH37) (CGI-70) (AD-019). [SWISSPROT;Acc:Q9Y5K5] 0.154436 UCHL5 0.250677951
0.0387861 1435 SPLICING COACTIVATOR SUBUNIT SRM300; RNA BINDING PROTEIN; AT-RICH ELEMENT BINDING FACTOR. [RefSeq;Acc:NM_016333] 0.159183 SRRM2 0.2436573
0.038802 3087 0.397415 FAM20A 0.097635972
0.0388043 2441 MYO-INOSITOL 1-PHOSPHATE SYNTHASE A1. [RefSeq;Acc:NM_016368] 0.178742 no value 0.217096709
2442 UBIQUITIN-LIKE PROTEIN GDX (UBIQUITIN-LIKE PROTEIN 4). [SWISSPROT;Acc:P11441] UBL4A
0.0388254 1613 MITOCHONDRIAL RIBOSOMAL PROTEIN L30 ISOFORM A. [RefSeq;Acc:NM_145212] 0.161954 MRPL30 0.239731035
0.0388692 1124 RNA POLYMERASE II SUBUNIT 5-MEDIATING PROTEIN (RPB5-MEDIATING PROTEIN). [SWISSPROT;Acc:O94763] 0.155056 C19orf2 0.250678465
0.0388966 1122 TRANSCRIPTION FACTOR IIB. [RefSeq;Acc:NM_013242] 0.155152 C16orf80 0.25069995899999997
0.0389051 1086 GDP-MANNOSE PYROPHOSPHORYLASE A; MANNOSE-1-PHOSPHATE GUANYLYLTRANSFERASE (GDP). [RefSeq;Acc:NM_013335] 0.154417 GMPPA 0.251948296
0.038917 3169 RIBOSOMAL PROTEIN S6 KINASE-LIKE 1. [RefSeq;Acc:NM_031464] 0.619812 no value 0.062788394
0.0389372 1960 PROTEIN 1-4 (ATP BINDING PROTEIN ASSOCIATED WITH CELL DIFFERENTIATION). [SWISSPROT;Acc:O14530] 0.1684 TXNDC9 0.231218527
0.0389719 377 0.139616 CCDC12 0.279136345
0.0391008 3042 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(O) GAMMA-7 SUBUNIT. [SWISSPROT;Acc:O60262] 0.366305 no value 0.106743834
3043 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(O) GAMMA-12 SUBUNIT. [SWISSPROT;Acc:Q9UBI6] GNG12
0.0391646 962 PRIP-INTERACTING PROTEIN PIPMT; PRIP-INTERACTING PROTEIN WITH METHYLTRANSFERASE DOMAIN. [RefSeq;Acc:NM_024831] 0.152962 TGS1 0.25604137
963 C6orf32
0.0391808 3200 RAS-RELATED GTP BINDING A; RAS-RELATED GTP-BINDING PROTEIN. [RefSeq;Acc:NM_006570] 1.63989 RRAGA 0.023892334
0.0391877 1351 HUMAN IMMUNODEFICIENCY VIRUS TYPE I ENHANCER BINDING PROTEIN 3. [RefSeq;Acc:NM_024503] 0.159829 HIVEP3 0.245185167
0.0392019 3054 "GUANINE NUCLEOTIDE-BINDING PROTEIN G(Y), ALPHA SUBUNIT (ALPHA-11). [SWISSPROT;Acc:P29992]" 0.371714 GNA11 0.105462533
0.0393162 1113 CARBOXYPEPTIDASE H PRECURSOR (EC 3.4.17.10) (CPH) (CARBOXYPEPTIDASE E) (CPE) (ENKEPHALIN CONVERTASE) (PROHORMONE PROCESSING CARBOXYPEPTIDASE). [SWISSPROT;Acc:P16870] 0.156752 CPE 0.250817852
0.0393961 1324 "28S RIBOSOMAL PROTEIN S26, MITOCHONDRIAL PRECURSOR (MRP-S26) (MRP- S13). [SWISSPROT;Acc:Q9BYN8]" 0.160458 MRPS26 0.245522816
1325 CHCHD4
0.039427 1887 PEPTIDYL PROLYL ISOMERASE H; CYCLOPHILIN H. [RefSeq;Acc:NM_006347] 0.1694 PPIH 0.232744982
0.0394801 1566 ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 1. [SWISSPROT;Acc:P40616] 0.163824 ARL1 0.240990941
1567 NEFA-INTERACTING NUCLEAR PROTEIN NIP30. [RefSeq;Acc:NM_024946] no value
0.0394844 456 0.143261 ZMAT2 0.275611646
0.0395353 2657 "SOLUTE CARRIER FAMILY 13, MEMBER 3 (SODIUM-DEPENDENT HIGH-AFFINITY DICARBOXYLATE TRANSPORTER 2) (NA(+)/DICARBOXYLATE COTRANSPORTER 3) (NADC-3) (HNADC3). [SWISSPROT;Acc:Q8WWT9]" 0.188319 SLC13A3 0.209937924
0.0395402 814 0.151289 EXDL2 0.261355419
0.0395834 3055 "GUANINE NUCLEOTIDE-BINDING PROTEIN G(Q), ALPHA SUBUNIT. [SWISSPROT;Acc:P50148]" 0.375337 GNAQ 0.105460959
0.0395897 981 60 KDA TAT INTERACTIVE PROTEIN (TIP60) (HIV-1 TAT INTERACTIVE PROTEIN) (CPLA(2) INTERACTING PROTEIN). [SWISSPROT;Acc:Q92993] 0.155084 HTATIP 0.255279075
0.0396993 343 0.139829 C16orf57 0.283913208
0.0397033 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]" 0.156754 no value 0.253284127
0.039713 878 PUTATIVE PRE-MRNA SPLICING FACTOR RNA HELICASE (ATP-DEPENDENT RNA HELICASE #3) (DEAH-BOX PROTEIN 16). [SWISSPROT;Acc:O60231] 0.15268 0.260106104
0.0397949 424 0.143472 ARHGAP23 0.277370497
0.0398119 2981 0.285269 MTERFD1 0.139559153
0.0398596 3086 PROPROTEIN CONVERTASE SUBTILISIN/KEXIN TYPE 5 PRECURSOR (EC 3.4.21.-) (PROPROTEIN CONVERTASE PC5) (SUBTILISIN/KEXIN-LIKE PROTEASE PC5) (CONVERTASE PC5) (PC6) (HPC6). [SWISSPROT;Acc:Q92824] 0.408247 PCSK5 0.09763599
0.0398851 727 ZINC FINGER PROTEIN 262; CELL DEATH INHIBITING RNA. [RefSeq;Acc:NM_005095] 0.150694 ZMYM4 0.264676099
728 CONSERVED OLIGOMERIC GOLGI COMPLEX COMPONENT 3 (VESICLE DOCKING PROTEIN SEC34 HOMOLOG) (P94). [SWISSPROT;Acc:Q96JB2] COG3
0.0399967 534 SMALL NUCLEAR RIBONUCLEOPROTEIN E (SNRNP-E) (SM PROTEIN E) (SM-E) (SME). [SWISSPROT;Acc:P08578] 0.14739 no value 0.271366443
0.040067 920 RAL-A EXCHANGE FACTOR RALGPS2. [RefSeq;Acc:NM_152663] 0.155337 RALGPS2 0.257935971
0.0401118 1295 0.163123 BUD13 0.245899107
1296 SIMILAR TO ECOTROPIC VIRAL INTEGRATION SITE 5; NEUROBLASTOMA STAGE 4S GENE. [RefSeq;Acc:NM_145245] EVI5L

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/