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 final Gene Rank expected Hugo description
Results: HTML CSV LaTeX Showing element 551 to 600 of 3206 in total
measured
final
Rank
expected
Hugo
description
0.0385694 0.264498255 742 0.145821 BBS7 BARDET-BIEDL SYNDROME 7 PROTEIN ISOFORM A; BBS2-LIKE 1. [RefSeq;Acc:NM_176824]
743 HSDL2
0.0386201 0.24860218 1191 0.155349 TBP TATA BOX BINDING PROTEIN (TRANSCRIPTION INITIATION FACTOR TFIID) (TATA-BOX FACTOR) (TATA SEQUENCE-BINDING PROTEIN) (TBP). [SWISSPROT;Acc:P20226]
1192 ATP13A4
0.0386224 0.225479596 2202 0.17129 NDST2 HEPARIN SULFATE N-DEACETYLASE/N-SULFOTRANSFERASE (EC 2.8.2.-) (N- HSST) (N-HEPARIN SULFATE SULFOTRANSFERASE) (GLUCOSAMINYL N- DEACETYLASE/N-SULFOTRANSFERASE). [SWISSPROT;Acc:P52849]
0.038631 0.243657992 1433 0.158546 no value RNA HELICASE-RELATED PROTEIN; RNA HELICASE-LIKE PROTEIN; SF3B125 DEAD-BOX PROTEIN. [RefSeq;Acc:NM_007372]
0.038682 0.228122217 2125 0.169567 TCP11L1
0.0387072 0.234553552 1807 0.165025 EEA1 "EARLY ENDOSOME ANTIGEN 1, 162KD; EARLY ENDOSOME-ASSOCIATED PROTEIN. [RefSeq;Acc:NM_003566]"
0.0387137 0.250677951 1126 0.154436 UCHL5 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]
0.0387861 0.2436573 1435 0.159183 SRRM2 SPLICING COACTIVATOR SUBUNIT SRM300; RNA BINDING PROTEIN; AT-RICH ELEMENT BINDING FACTOR. [RefSeq;Acc:NM_016333]
0.038802 0.097635972 3087 0.397415 FAM20A
0.0388043 0.217096709 2441 0.178742 no value MYO-INOSITOL 1-PHOSPHATE SYNTHASE A1. [RefSeq;Acc:NM_016368]
2442 UBL4A UBIQUITIN-LIKE PROTEIN GDX (UBIQUITIN-LIKE PROTEIN 4). [SWISSPROT;Acc:P11441]
0.0388254 0.239731035 1613 0.161954 MRPL30 MITOCHONDRIAL RIBOSOMAL PROTEIN L30 ISOFORM A. [RefSeq;Acc:NM_145212]
0.0388692 0.250678465 1124 0.155056 C19orf2 RNA POLYMERASE II SUBUNIT 5-MEDIATING PROTEIN (RPB5-MEDIATING PROTEIN). [SWISSPROT;Acc:O94763]
0.0388966 0.25069995899999997 1122 0.155152 C16orf80 TRANSCRIPTION FACTOR IIB. [RefSeq;Acc:NM_013242]
0.0389051 0.251948296 1086 0.154417 GMPPA GDP-MANNOSE PYROPHOSPHORYLASE A; MANNOSE-1-PHOSPHATE GUANYLYLTRANSFERASE (GDP). [RefSeq;Acc:NM_013335]
0.038917 0.062788394 3169 0.619812 no value RIBOSOMAL PROTEIN S6 KINASE-LIKE 1. [RefSeq;Acc:NM_031464]
0.0389372 0.231218527 1960 0.1684 TXNDC9 PROTEIN 1-4 (ATP BINDING PROTEIN ASSOCIATED WITH CELL DIFFERENTIATION). [SWISSPROT;Acc:O14530]
0.0389719 0.279136345 377 0.139616 CCDC12
0.0391008 0.106743834 3042 0.366305 no value GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(O) GAMMA-7 SUBUNIT. [SWISSPROT;Acc:O60262]
3043 GNG12 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(O) GAMMA-12 SUBUNIT. [SWISSPROT;Acc:Q9UBI6]
0.0391646 0.25604137 962 0.152962 TGS1 PRIP-INTERACTING PROTEIN PIPMT; PRIP-INTERACTING PROTEIN WITH METHYLTRANSFERASE DOMAIN. [RefSeq;Acc:NM_024831]
963 C6orf32
0.0391808 0.023892334 3200 1.63989 RRAGA RAS-RELATED GTP BINDING A; RAS-RELATED GTP-BINDING PROTEIN. [RefSeq;Acc:NM_006570]
0.0391877 0.245185167 1351 0.159829 HIVEP3 HUMAN IMMUNODEFICIENCY VIRUS TYPE I ENHANCER BINDING PROTEIN 3. [RefSeq;Acc:NM_024503]
0.0392019 0.105462533 3054 0.371714 GNA11 "GUANINE NUCLEOTIDE-BINDING PROTEIN G(Y), ALPHA SUBUNIT (ALPHA-11). [SWISSPROT;Acc:P29992]"
0.0393162 0.250817852 1113 0.156752 CPE CARBOXYPEPTIDASE H PRECURSOR (EC 3.4.17.10) (CPH) (CARBOXYPEPTIDASE E) (CPE) (ENKEPHALIN CONVERTASE) (PROHORMONE PROCESSING CARBOXYPEPTIDASE). [SWISSPROT;Acc:P16870]
0.0393961 0.245522816 1324 0.160458 MRPS26 "28S RIBOSOMAL PROTEIN S26, MITOCHONDRIAL PRECURSOR (MRP-S26) (MRP- S13). [SWISSPROT;Acc:Q9BYN8]"
1325 CHCHD4
0.039427 0.232744982 1887 0.1694 PPIH PEPTIDYL PROLYL ISOMERASE H; CYCLOPHILIN H. [RefSeq;Acc:NM_006347]
0.0394801 0.240990941 1566 0.163824 ARL1 ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 1. [SWISSPROT;Acc:P40616]
1567 no value NEFA-INTERACTING NUCLEAR PROTEIN NIP30. [RefSeq;Acc:NM_024946]
0.0394844 0.275611646 456 0.143261 ZMAT2
0.0395353 0.209937924 2657 0.188319 SLC13A3 "SOLUTE CARRIER FAMILY 13, MEMBER 3 (SODIUM-DEPENDENT HIGH-AFFINITY DICARBOXYLATE TRANSPORTER 2) (NA(+)/DICARBOXYLATE COTRANSPORTER 3) (NADC-3) (HNADC3). [SWISSPROT;Acc:Q8WWT9]"
0.0395402 0.261355419 814 0.151289 EXDL2
0.0395834 0.105460959 3055 0.375337 GNAQ "GUANINE NUCLEOTIDE-BINDING PROTEIN G(Q), ALPHA SUBUNIT. [SWISSPROT;Acc:P50148]"
0.0395897 0.255279075 981 0.155084 HTATIP 60 KDA TAT INTERACTIVE PROTEIN (TIP60) (HIV-1 TAT INTERACTIVE PROTEIN) (CPLA(2) INTERACTING PROTEIN). [SWISSPROT;Acc:Q92993]
0.0396993 0.283913208 343 0.139829 C16orf57
0.0397033 0.253284127 1040 0.156754 no value "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]"
0.039713 0.260106104 878 0.15268 PUTATIVE PRE-MRNA SPLICING FACTOR RNA HELICASE (ATP-DEPENDENT RNA HELICASE #3) (DEAH-BOX PROTEIN 16). [SWISSPROT;Acc:O60231]
0.0397949 0.277370497 424 0.143472 ARHGAP23
0.0398119 0.139559153 2981 0.285269 MTERFD1
0.0398596 0.09763599 3086 0.408247 PCSK5 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]
0.0398851 0.264676099 727 0.150694 ZMYM4 ZINC FINGER PROTEIN 262; CELL DEATH INHIBITING RNA. [RefSeq;Acc:NM_005095]
728 COG3 CONSERVED OLIGOMERIC GOLGI COMPLEX COMPONENT 3 (VESICLE DOCKING PROTEIN SEC34 HOMOLOG) (P94). [SWISSPROT;Acc:Q96JB2]
0.0399967 0.271366443 534 0.14739 no value SMALL NUCLEAR RIBONUCLEOPROTEIN E (SNRNP-E) (SM PROTEIN E) (SM-E) (SME). [SWISSPROT;Acc:P08578]
0.040067 0.257935971 920 0.155337 RALGPS2 RAL-A EXCHANGE FACTOR RALGPS2. [RefSeq;Acc:NM_152663]
0.0401118 0.245899107 1295 0.163123 BUD13
1296 EVI5L SIMILAR TO ECOTROPIC VIRAL INTEGRATION SITE 5; NEUROBLASTOMA STAGE 4S GENE. [RefSeq;Acc:NM_145245]

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/