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 Hugo description expected final
Results: HTML CSV LaTeX Showing element 302 to 351 of 3206 in total
measured
Rank
Hugo
description
expected
final
0.0308958 2261 ATPAF1 0.138512 0.223055042
0.0309189 2254 C7orf24 0.138615 0.223055946
0.030934 730 ZMYM3 ZINC FINGER PROTEIN 261 (DXS6673E PROTEIN). [SWISSPROT;Acc:Q14202] 0.116875 0.264675936
0.0310206 2888 DPP8 DIPEPTIDYL PEPTIDASE 8 ISOFORM 2; DIPEPTIDYL PEPTIDASE 8. [RefSeq;Acc:NM_017743] 0.172385 0.179949532
0.0310375 811 no value BRAIN PROTEIN 16. [RefSeq;Acc:NM_016458] 0.118668 0.261549028
0.0310799 2983 HOMEOBOX PROTEIN HOX-A4 (HOX-1D) (HOX-1.4). [SWISSPROT;Acc:Q00056] 0.222701 0.13955887
0.0311291 3186 FCN2 FICOLIN 2 PRECURSOR (COLLAGEN/FIBRINOGEN DOMAIN-CONTAINING PROTEIN 2) (FICOLIN-B) (FICOLIN B) (SERUM LECTIN P35) (EBP-37) (HUCOLIN) (L- FICOLIN). [SWISSPROT;Acc:Q15485] 0.834222 0.037315127
0.0311395 2974 HOXD4 HOMEOBOX PROTEIN HOX-D4 (HOX-4B) (HOX-5.1) (HHO.C13). [SWISSPROT;Acc:P09016] 0.223127 0.139559533
0.0311416 807 MRPL28 MELANOMA ANTIGEN P15 (MELANOMA-ASSOCIATED ANTIGEN RECOGNIZED BY T LYMPHOCYTES). [SWISSPROT;Acc:Q13084] 0.118856 0.262011173
0.0311669 731 ZMYM2 ZINC FINGER PROTEIN 198 (FUSED IN MYELOPROLIFERATIVE DISORDERS PROTEIN) (REARRANGED IN ATYPICAL MYELOPROLIFERATIVE DISORDER PROTEIN). [SWISSPROT;Acc:Q9UBW7] 0.117755 0.26467581
0.0311675 1262 SHQ1 0.126112 0.24714143
0.0311751 2539 DPP6 DIPEPTIDYL AMINOPEPTIDASE-LIKE PROTEIN 6 (DIPEPTIDYLPEPTIDASE VI) (DIPEPTIDYLPEPTIDASE 6) (DIPEPTIDYL PEPTIDASE IV LIKE PROTEIN) (DIPEPTIDYL AMINOPEPTIDASE-RELATED PROTEIN) (DPPX). [SWISSPROT;Acc:P42658] 0.145258 0.214618816
0.0311872 2976 no value HOMEOBOX PROTEIN HOX-C4 (HOX-3E) (CP19). [SWISSPROT;Acc:P09017] 0.223469 0.139559402
0.0311972 1696 SLC25A6 "ADP,ATP CARRIER PROTEIN, LIVER ISOFORM T2 (ADP/ATP TRANSLOCASE 3) (ADENINE NUCLEOTIDE TRANSLOCATOR 3) (ANT 3). [SWISSPROT;Acc:P12236]" 0.131153 0.237868749
0.0312313 2866 no value HEPATOMA-DERIVED GROWTH FACTOR-RELATED PROTEIN 2. [RefSeq;Acc:NM_032631] 0.165297 0.188940513
0.0312503 1601 TSNAX TRANSLIN-ASSOCIATED PROTEIN X (TRANSLIN-ASSOCIATED FACTOR X). [SWISSPROT;Acc:Q99598] 0.130205 0.240008448
1602 PQBP1 POLYGLUTAMINE BINDING PROTEIN 1; NUCLEAR PROTEIN CONTAINING WW DOMAIN 38 KD. [RefSeq;Acc:NM_005710]
0.0312821 3049 no value GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(O) GAMMA-5 LIKE SUBUNIT. [SWISSPROT;Acc:Q9Y3K8] 0.293231 0.10668074
0.0312832 798 TMCC3 0.119396 0.262012128
0.0313105 3179 CUL1 CULLIN HOMOLOG 1 (CUL-1). [SWISSPROT;Acc:Q13616] 0.629022 0.049776478
3180 PSEN1 PRESENILIN 1 (PS-1) (S182 PROTEIN). [SWISSPROT;Acc:P49768]
0.031325 2088 no value 0.13696 0.228716414
0.0313429 2870 HDGF HEPATOMA-DERIVED GROWTH FACTOR (HDGF) (HIGH-MOBILITY GROUP PROTEIN 1- LIKE 2) (HMG-1L2). [SWISSPROT;Acc:P51858] 0.165888 0.188940128
0.0313539 2982 HOXB4 HOMEOBOX PROTEIN HOX-B4 (HOX-2F) (HOX-2.6). [SWISSPROT;Acc:P17483] 0.224664 0.139559075
0.0313747 2723 no value 0.1519 0.206548387
0.0314375 2528 KERATIN ASSOCIATED PROTEIN 4-2; KERATIN ASSOCIATED PROTEIN 4.2. [RefSeq;Acc:NM_033062] 0.146383 0.21476196
0.031449 1863 DOLK 0.134819 0.233268308
0.0314533 1406 CYCS CYTOCHROME C. [SWISSPROT;Acc:P00001] 0.128904 0.244005617
1407 HS6ST1 HEPARAN SULFATE 6-O-SULFOTRANSFERASE; HEPARAN-SULFATE 6-SULFOTRANSFERASE. [RefSeq;Acc:NM_004807]
0.0314703 2445 UBL4B 0.14496 0.21709644
0.0315458 2056 COQ10A 0.137326 0.229714694
0.031557 3196 CHMP4B 0.85608 0.036862209
0.0315727 1741 COTL1 COACTOSIN-LIKE PROTEIN. [SWISSPROT;Acc:Q14019] 0.133236 0.236968237
0.0315866 1930 CWF19L2 0.136317 0.231714313
0.0315995 1422 PCID2 0.129562 0.243894815
0.031639 1423 no value NUCLEAR RECEPTOR CO-REPRESSOR/HDAC3 COMPLEX SUBUNIT TBLR1 (TBL1- RELATED PROTEIN 1). [SWISSPROT;Acc:Q9BZK7] 0.129724 0.24389473
0.0316607 2204 NDST3 N-DEACETYLASE/N-SULFOTRANSFERASE (HEPARAN GLUCOSAMINYL) 3. [RefSeq;Acc:NM_004784] 0.140415 0.225479472
0.031665 3048 GNG10 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(O) GAMMA-10 SUBUNIT. [SWISSPROT;Acc:P50151] 0.29681 0.106684411
0.0317084 1292 EVI5 ECOTROPIC VIRAL INTEGRATION SITE 5; NEUROBLASTOMA STAGE 4S GENE. [RefSeq;Acc:NM_005665] 0.128948 0.245900673
0.031735 964 SSRP1 STRUCTURE-SPECIFIC RECOGNITION PROTEIN 1 (SSRP1) (RECOMBINATION SIGNAL SEQUENCE RECOGNITION PROTEIN) (T160) (CHROMATIN-SPECIFIC TRANSCRIPTION ELONGATION FACTOR 80 KDA SUBUNIT) (FACT 80 KDA SUBUNIT). [SWISSPROT;Acc:Q08945] 0.124 0.255927419
0.0317441 720 ZMYM6 ZINC FINGER PROTEIN 258. [RefSeq;Acc:NM_145310] 0.119935 0.264677534
0.0317812 749 SLMO1 ERYTHROID DIFFERENTIATION AND DENUCLEATION FACTOR 1. [SWISSPROT;Acc:O60584] 0.120157 0.264497283
0.0317927 3047 GNG5 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(O) GAMMA-5 SUBUNIT. [SWISSPROT;Acc:P30670] 0.298003 0.106685839
0.031831 2538 DPP10 DIPEPTIDYLPEPTIDASE 10; DIPEPTIDYL PEPTIDASE IV-RELATED PROTEIN 3. [RefSeq;Acc:NM_020868] 0.148314 0.214618984
0.0318436 3189 MFAP4 MICROFIBRIL-ASSOCIATED GLYCOPROTEIN 4 PRECURSOR. [SWISSPROT;Acc:P55083] 0.853372 0.037315028
0.0318532 1268 SIM1 SINGLE-MINDED HOMOLOG 1. [SWISSPROT;Acc:P81133] 0.12912 0.246694548
0.0319117 2205 NDST4 N-DEACETYLASE/N-SULFOTRANSFERASE 4. [RefSeq;Acc:NM_022569] 0.141529 0.225478171
0.0319409 1779 RDH8 RETINOL DEHYDROGENASE 8 (ALL-TRANS); PHOTORECEPTOR OUTER SEGMENT ALL-TRANS RETINOL DEHYDROGENASE. [RefSeq;Acc:NM_015725] 0.135713 0.23535623
0.0319701 707 RCOR2 0.120575 0.265147004
0.0319827 2650 VPS35 VACUOLAR PROTEIN SORTING 35 (VESICLE PROTEIN SORTING 35) (HVPS35) (MATERNAL-EMBRYONIC 3). [SWISSPROT;Acc:Q96QK1] 0.152326 0.209962186

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/