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 Rank Gene description expected Hugo final
Results: HTML CSV LaTeX Showing element 301 to 350 of 3206 in total
measured
Rank
description
expected
Hugo
final
0.0308872 2869 PC4 AND SFRS1 INTERACTING PROTEIN 2; PC4 AND SFRS1 INTERACTING PROTEIN 1; TRANSCRIPTIONAL COACTIVATOR P52/P75. [RefSeq;Acc:NM_033222] 0.163476 PSIP1 0.188940273
0.0308958 2261 0.138512 ATPAF1 0.223055042
0.0309189 2254 0.138615 C7orf24 0.223055946
0.030934 730 ZINC FINGER PROTEIN 261 (DXS6673E PROTEIN). [SWISSPROT;Acc:Q14202] 0.116875 ZMYM3 0.264675936
0.0310206 2888 DIPEPTIDYL PEPTIDASE 8 ISOFORM 2; DIPEPTIDYL PEPTIDASE 8. [RefSeq;Acc:NM_017743] 0.172385 DPP8 0.179949532
0.0310375 811 BRAIN PROTEIN 16. [RefSeq;Acc:NM_016458] 0.118668 no value 0.261549028
0.0310799 2983 HOMEOBOX PROTEIN HOX-A4 (HOX-1D) (HOX-1.4). [SWISSPROT;Acc:Q00056] 0.222701 0.13955887
0.0311291 3186 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 FCN2 0.037315127
0.0311395 2974 HOMEOBOX PROTEIN HOX-D4 (HOX-4B) (HOX-5.1) (HHO.C13). [SWISSPROT;Acc:P09016] 0.223127 HOXD4 0.139559533
0.0311416 807 MELANOMA ANTIGEN P15 (MELANOMA-ASSOCIATED ANTIGEN RECOGNIZED BY T LYMPHOCYTES). [SWISSPROT;Acc:Q13084] 0.118856 MRPL28 0.262011173
0.0311669 731 ZINC FINGER PROTEIN 198 (FUSED IN MYELOPROLIFERATIVE DISORDERS PROTEIN) (REARRANGED IN ATYPICAL MYELOPROLIFERATIVE DISORDER PROTEIN). [SWISSPROT;Acc:Q9UBW7] 0.117755 ZMYM2 0.26467581
0.0311675 1262 0.126112 SHQ1 0.24714143
0.0311751 2539 DIPEPTIDYL AMINOPEPTIDASE-LIKE PROTEIN 6 (DIPEPTIDYLPEPTIDASE VI) (DIPEPTIDYLPEPTIDASE 6) (DIPEPTIDYL PEPTIDASE IV LIKE PROTEIN) (DIPEPTIDYL AMINOPEPTIDASE-RELATED PROTEIN) (DPPX). [SWISSPROT;Acc:P42658] 0.145258 DPP6 0.214618816
0.0311872 2976 HOMEOBOX PROTEIN HOX-C4 (HOX-3E) (CP19). [SWISSPROT;Acc:P09017] 0.223469 no value 0.139559402
0.0311972 1696 "ADP,ATP CARRIER PROTEIN, LIVER ISOFORM T2 (ADP/ATP TRANSLOCASE 3) (ADENINE NUCLEOTIDE TRANSLOCATOR 3) (ANT 3). [SWISSPROT;Acc:P12236]" 0.131153 SLC25A6 0.237868749
0.0312313 2866 HEPATOMA-DERIVED GROWTH FACTOR-RELATED PROTEIN 2. [RefSeq;Acc:NM_032631] 0.165297 no value 0.188940513
0.0312503 1601 TRANSLIN-ASSOCIATED PROTEIN X (TRANSLIN-ASSOCIATED FACTOR X). [SWISSPROT;Acc:Q99598] 0.130205 TSNAX 0.240008448
1602 POLYGLUTAMINE BINDING PROTEIN 1; NUCLEAR PROTEIN CONTAINING WW DOMAIN 38 KD. [RefSeq;Acc:NM_005710] PQBP1
0.0312821 3049 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(O) GAMMA-5 LIKE SUBUNIT. [SWISSPROT;Acc:Q9Y3K8] 0.293231 no value 0.10668074
0.0312832 798 0.119396 TMCC3 0.262012128
0.0313105 3179 CULLIN HOMOLOG 1 (CUL-1). [SWISSPROT;Acc:Q13616] 0.629022 CUL1 0.049776478
3180 PRESENILIN 1 (PS-1) (S182 PROTEIN). [SWISSPROT;Acc:P49768] PSEN1
0.031325 2088 0.13696 no value 0.228716414
0.0313429 2870 HEPATOMA-DERIVED GROWTH FACTOR (HDGF) (HIGH-MOBILITY GROUP PROTEIN 1- LIKE 2) (HMG-1L2). [SWISSPROT;Acc:P51858] 0.165888 HDGF 0.188940128
0.0313539 2982 HOMEOBOX PROTEIN HOX-B4 (HOX-2F) (HOX-2.6). [SWISSPROT;Acc:P17483] 0.224664 HOXB4 0.139559075
0.0313747 2723 0.1519 no value 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 0.134819 DOLK 0.233268308
0.0314533 1406 CYTOCHROME C. [SWISSPROT;Acc:P00001] 0.128904 CYCS 0.244005617
1407 HEPARAN SULFATE 6-O-SULFOTRANSFERASE; HEPARAN-SULFATE 6-SULFOTRANSFERASE. [RefSeq;Acc:NM_004807] HS6ST1
0.0314703 2445 0.14496 UBL4B 0.21709644
0.0315458 2056 0.137326 COQ10A 0.229714694
0.031557 3196 0.85608 CHMP4B 0.036862209
0.0315727 1741 COACTOSIN-LIKE PROTEIN. [SWISSPROT;Acc:Q14019] 0.133236 COTL1 0.236968237
0.0315866 1930 0.136317 CWF19L2 0.231714313
0.0315995 1422 0.129562 PCID2 0.243894815
0.031639 1423 NUCLEAR RECEPTOR CO-REPRESSOR/HDAC3 COMPLEX SUBUNIT TBLR1 (TBL1- RELATED PROTEIN 1). [SWISSPROT;Acc:Q9BZK7] 0.129724 no value 0.24389473
0.0316607 2204 N-DEACETYLASE/N-SULFOTRANSFERASE (HEPARAN GLUCOSAMINYL) 3. [RefSeq;Acc:NM_004784] 0.140415 NDST3 0.225479472
0.031665 3048 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(O) GAMMA-10 SUBUNIT. [SWISSPROT;Acc:P50151] 0.29681 GNG10 0.106684411
0.0317084 1292 ECOTROPIC VIRAL INTEGRATION SITE 5; NEUROBLASTOMA STAGE 4S GENE. [RefSeq;Acc:NM_005665] 0.128948 EVI5 0.245900673
0.031735 964 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 SSRP1 0.255927419
0.0317441 720 ZINC FINGER PROTEIN 258. [RefSeq;Acc:NM_145310] 0.119935 ZMYM6 0.264677534
0.0317812 749 ERYTHROID DIFFERENTIATION AND DENUCLEATION FACTOR 1. [SWISSPROT;Acc:O60584] 0.120157 SLMO1 0.264497283
0.0317927 3047 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(O) GAMMA-5 SUBUNIT. [SWISSPROT;Acc:P30670] 0.298003 GNG5 0.106685839
0.031831 2538 DIPEPTIDYLPEPTIDASE 10; DIPEPTIDYL PEPTIDASE IV-RELATED PROTEIN 3. [RefSeq;Acc:NM_020868] 0.148314 DPP10 0.214618984
0.0318436 3189 MICROFIBRIL-ASSOCIATED GLYCOPROTEIN 4 PRECURSOR. [SWISSPROT;Acc:P55083] 0.853372 MFAP4 0.037315028
0.0318532 1268 SINGLE-MINDED HOMOLOG 1. [SWISSPROT;Acc:P81133] 0.12912 SIM1 0.246694548
0.0319117 2205 N-DEACETYLASE/N-SULFOTRANSFERASE 4. [RefSeq;Acc:NM_022569] 0.141529 NDST4 0.225478171
0.0319409 1779 RETINOL DEHYDROGENASE 8 (ALL-TRANS); PHOTORECEPTOR OUTER SEGMENT ALL-TRANS RETINOL DEHYDROGENASE. [RefSeq;Acc:NM_015725] 0.135713 RDH8 0.23535623
0.0319701 707 0.120575 RCOR2 0.265147004

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/