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