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 expected measured Hugo final description Rank
Results: HTML CSV LaTeX Showing element 451 to 500 of 3206 in total
expected
measured
Hugo
final
description
Rank
0.152533 0.0491097 PABPC4 0.321961149 POLYADENYLATE-BINDING PROTEIN 4 (POLY(A)-BINDING PROTEIN 4) (PABP 4) (INDUCIBLE POLY(A)-BINDING PROTEIN) (IPABP) (ACTIVATED-PLATELET PROTEIN-1) (APP-1). [SWISSPROT;Acc:Q13310] 201
0.15268 0.039713 no value 0.260106104 PUTATIVE PRE-MRNA SPLICING FACTOR RNA HELICASE (ATP-DEPENDENT RNA HELICASE #3) (DEAH-BOX PROTEIN 16). [SWISSPROT;Acc:O60231] 878
0.152757 0.0620387 ABLIM2 0.406126724 ACTIN BINDING LIM PROTEIN 2. [RefSeq;Acc:NM_032432] 71
0.15287 0.0421286 COL4A3 0.275584484 COLLAGEN ALPHA 3(IV) CHAIN PRECURSOR (GOODPASTURE ANTIGEN). [SWISSPROT;Acc:Q01955] 459
0.152962 0.0391646 C6orf32 0.25604137 963
TGS1 PRIP-INTERACTING PROTEIN PIPMT; PRIP-INTERACTING PROTEIN WITH METHYLTRANSFERASE DOMAIN. [RefSeq;Acc:NM_024831] 962
0.153258 0.0462548 FABP3 0.30181002 "FATTY ACID-BINDING PROTEIN, HEART (H-FABP) (MUSCLE FATTY ACID-BINDING PROTEIN) (M-FABP) (MAMMARY-DERIVED GROWTH INHIBITOR) (MDGI). [SWISSPROT;Acc:P05413]" 286
0.153273 0.0375954 FAM50B 0.245283905 DNA SEGMENT ON CHROMOSOME 6(UNIQUE) 2654 EXPRESSED SEQUENCE; DNA SEGMENT ON CHROMOSOME X (UNIQUE) 2654 EXPRESSED SEQUENCE. [RefSeq;Acc:NM_012135] 1337
0.153323 0.0207502 HS3ST2 0.135336512 HEPARAN SULFATE D-GLUCOSAMINYL 3-O-SULFOTRANSFERASE 2; HEPARIN-GLUCOSAMINE 3-O-SULFOTRANSFERASE. [RefSeq;Acc:NM_006043] 2991
0.153758 0.0385624 GTDC1 0.250799308 1119
0.153963 0.0361228 COG7 0.234620006 CONSERVED OLIGOMERIC GOLGI COMPLEX COMPONENT 7. [SWISSPROT;Acc:P83436] 1804
0.154417 0.0389051 GMPPA 0.251948296 GDP-MANNOSE PYROPHOSPHORYLASE A; MANNOSE-1-PHOSPHATE GUANYLYLTRANSFERASE (GDP). [RefSeq;Acc:NM_013335] 1086
0.154436 0.0387137 UCHL5 0.250677951 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] 1126
0.154523 0.037776 no value 0.244468461 BA271B5.1 (SIMILAR TO RIBOSOMAL PROTEIN S7). [SPTREMBL;Acc:Q9H1S9] 1386
0.154573 0.0350787 AMMECR1 0.226939375 AMMECR1 PROTEIN. [RefSeq;Acc:NM_015365] 2177
RAE1 MRNA-ASSOCIATED PROTEIN MRNP 41 (RAE1 PROTEIN HOMOLOG). [SWISSPROT;Acc:P78406] 2176
SCYL1 SCY1-LIKE 1; TELOMERASE REGULATION-ASSOCIATED PROTEIN; HT019 PROTEIN; TELOMERASE REGULATION-ASSOCIATED PROTEIN; N-TERMINAL KINASE-LIKE PROTEIN; TERATOMA-ASSOCIATED TYROSINE KINASE; N-TERMINAL KINASE-LIKE. [RefSeq;Acc:NM_020680] 2174
TMF1 TATA ELEMENT MODULATORY FACTOR (TMF). [SWISSPROT;Acc:P82094] 2175
0.154846 0.0415188 no value 0.268129626 644
0.155056 0.0388692 C19orf2 0.250678465 RNA POLYMERASE II SUBUNIT 5-MEDIATING PROTEIN (RPB5-MEDIATING PROTEIN). [SWISSPROT;Acc:O94763] 1124
0.15506 0.0544673 CCDC95 0.351265962 153
PBK T-LAK CELL-ORIGINATED PROTEIN KINASE; SPERMATOGENESIS-RELATED PROTEIN KINASE; PDZ-BINDING KINASE; PBK; MAPKK-LIKE PROTEIN KINASE; SERINE/THREONINE PROTEIN KINASE. [RefSeq;Acc:NM_018492] 152
0.155084 0.0395897 HTATIP 0.255279075 60 KDA TAT INTERACTIVE PROTEIN (TIP60) (HIV-1 TAT INTERACTIVE PROTEIN) (CPLA(2) INTERACTING PROTEIN). [SWISSPROT;Acc:Q92993] 981
0.155117 0.036083 MAP4 0.232617959 MICROTUBULE-ASSOCIATED PROTEIN 4 (MAP 4). [SWISSPROT;Acc:P27816] 1895
0.155152 0.0388966 C16orf80 0.25069995899999997 TRANSCRIPTION FACTOR IIB. [RefSeq;Acc:NM_013242] 1122
0.155207 0.0210051 HS3ST6 0.135336035 C439A6.1 (NOVEL PROTEIN SIMILAR TO HEPARAN SULFATE (GLUCOSAMINE) 3-O- SULFOTRANSFERASES) (FRAGMENT). [SPTREMBL;Acc:Q96QI5] 2995
0.155337 0.040067 RALGPS2 0.257935971 RAL-A EXCHANGE FACTOR RALGPS2. [RefSeq;Acc:NM_152663] 920
0.155349 0.0386201 ATP13A4 0.24860218 1192
TBP TATA BOX BINDING PROTEIN (TRANSCRIPTION INITIATION FACTOR TFIID) (TATA-BOX FACTOR) (TATA SEQUENCE-BINDING PROTEIN) (TBP). [SWISSPROT;Acc:P20226] 1191
0.155406 0.0406169 no value 0.261359922 DEAD-BOX PROTEIN ABSTRAKT HOMOLOG. [SWISSPROT;Acc:Q9UJV9] 813
0.155451 0.0333153 0.214313835 METABOTROPIC GLUTAMATE RECEPTOR 3 PRECURSOR (MGLUR3). [SWISSPROT;Acc:Q14832] 2555
C1orf26 2556
0.155504 0.0210454 HS3ST4 0.135336712 2990
0.155511 0.0337015 FRG1 0.216714573 FRG1 PROTEIN (FSHD REGION GENE 1 PROTEIN). [SWISSPROT;Acc:Q14331] 2462
RPAP1 2461
TADA3L TRANSCRIPTIONAL ADAPTOR 3-LIKE ISOFORM A. [RefSeq;Acc:NM_006354] 2463
0.155595 0.0403612 TEX9 0.259399081 900
0.155797 0.0294363 HDGFL1 0.188940095 PWWP DOMAIN CONTAINING 1; HDGF (HEPATOMA-DERIVED GROWTH FACTOR) LIKE. [RefSeq;Acc:NM_138574] 2871
0.155989 0.0384625 no value 0.246571874 KAPPA B-RAS 1. [RefSeq;Acc:NM_020345] 1273
SNAPAP SNARE ASSOCIATED PROTEIN SNAPIN. [RefSeq;Acc:NM_012437] 1274
0.156155 0.03729 C10orf83 0.238801191 44050 PROTEIN. [RefSeq;Acc:NM_178832] 1666
0.156164 0.0344025 PCDH15 0.220297252 PROTOCADHERIN 15 PRECURSOR. [SWISSPROT;Acc:Q96QU1] 2358
0.156176 0.037683 C21orf66 0.241285473 GC-RICH SEQUENCE DNA-BINDING FACTOR HOMOLOG. [SWISSPROT;Acc:Q9Y5B6] 1558
TLR2 TOLL-LIKE RECEPTOR 2 PRECURSOR (TOLL/INTERLEUKIN 1 RECEPTOR-LIKE PROTEIN 4). [SWISSPROT;Acc:O60603] 1559
0.156638 0.038293 RPS7 0.244468137 40S RIBOSOMAL PROTEIN S7 (S8). [SWISSPROT;Acc:P23821] 1388
0.156752 0.0393162 CPE 0.250817852 CARBOXYPEPTIDASE H PRECURSOR (EC 3.4.17.10) (CPH) (CARBOXYPEPTIDASE E) (CPE) (ENKEPHALIN CONVERTASE) (PROHORMONE PROCESSING CARBOXYPEPTIDASE). [SWISSPROT;Acc:P16870] 1113
0.156754 0.0397033 no value 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]" 1040
0.156874 0.0637106 ABLIM3 0.406125935 77
0.157168 0.06383 no value 0.406125929 ASPARTATE BETA-HYDROXYLASE ISOFORM B; JUNCTIN ISOFORM 1; JUNCTATE; ASPARTYL/ASPARAGINYL-BETA-HYDROXYLASE; PEPTIDE-ASPARTATE BETA-DIOXYGENASE; HUMBUG. [RefSeq;Acc:NM_032468] 78
0.157255 0.038432 WDR82 0.244392865 1392

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/