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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measured Gene Rank description Hugo expected final
Results: HTML CSV LaTeX Showing element 3058 to 3107 of 3206 in total
measured
Rank
description
Hugo
expected
final
0.753893 994 PROTEASOME SUBUNIT BETA TYPE 4 PRECURSOR (EC 3.4.25.1) (PROTEASOME BETA CHAIN) (MACROPAIN BETA CHAIN) (MULTICATALYTIC ENDOPEPTIDASE COMPLEX BETA CHAIN) (PROTEASOME CHAIN 3) (HSN3) (HSBPROS26). [SWISSPROT;Acc:P28070] PSMB4 2.95595 0.255042541
0.754507 2722 PROLIFERATING CELL NUCLEAR ANTIGEN (PCNA) (CYCLIN). [SWISSPROT;Acc:P12004] PCNA 3.65293 0.206548442
0.755644 250 ALPHA-NAC PROTEIN. [SPTREMBL;Acc:Q9H009] no value 2.42272 0.311899023
0.75685 1654 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 13 (26S PROTEASOME REGULATORY SUBUNIT S11) (26S PROTEASOME REGULATORY SUBUNIT P40.5). [SWISSPROT;Acc:Q9UNM6] PSMD13 3.16764 0.238931823
0.761536 2007 EUKARYOTIC TRANSLATION INITIATION FACTOR 2 SUBUNIT 1 (EUKARYOTIC TRANSLATION INITIATION FACTOR 2 ALPHA SUBUNIT) (EIF-2-ALPHA) (EIF- 2ALPHA) (EIF-2A). [SWISSPROT;Acc:P05198] EIF2S1 3.30114 0.230688792
0.762918 1222 DYSTROBREVIN ALPHA (DYSTROBREVIN-ALPHA). [SWISSPROT;Acc:Q9Y4J8] DTNA 3.07607 0.248017113
0.764466 225 SPLICING FACTOR 3B SUBUNIT 1 (SPLICEOSOME ASSOCIATED PROTEIN 155) (SAP 155) (SF3B155) (PRE-MRNA SPLICING FACTOR SF3B 155 KDA SUBUNIT). [SWISSPROT;Acc:O75533] SF3B1 2.41141 0.317020333
0.766353 1638 26S PROTEASE REGULATORY SUBUNIT 6A (TAT-BINDING PROTEIN 1) (TBP-1) (PROTEASOME SUBUNIT P50). [SWISSPROT;Acc:P17980] PSMC3 3.20427 0.239166175
0.771001 193 B9 PROTEIN; LIKELY ORTHOLOG OF MOUSE ENDOTHELIAL PRECURSOR PROTEIN B9. [RefSeq;Acc:NM_015681] B9D1 2.3671 0.325715432
0.771753 1150 PROTEASOME SUBUNIT BETA TYPE 1 (EC 3.4.25.1) (PROTEASOME COMPONENT C5) (MACROPAIN SUBUNIT C5) (MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT C5) (PROTEASOME GAMMA CHAIN). [SWISSPROT;Acc:P20618] PSMB1 3.08939 0.249807567
0.779006 1360 PROTEASOME SUBUNIT BETA TYPE 5 PRECURSOR (EC 3.4.25.1) (PROTEASOME EPSILON CHAIN) (MACROPAIN EPSILON CHAIN) (MULTICATALYTIC ENDOPEPTIDASE COMPLEX EPSILON CHAIN) (PROTEASOME SUBUNIT X) (PROTEASOME CHAIN 6) (PROTEASOME SUBUNIT MB1). [SWISSPROT;Acc:P2 PSMB5 3.17883 0.245060604
0.779642 1703 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 3 (26S PROTEASOME REGULATORY SUBUNIT S3) (PROTEASOME SUBUNIT P58). [SWISSPROT;Acc:O43242] PSMD3 3.27908 0.237762421
0.781534 1157 PROTEASOME SUBUNIT BETA TYPE 3 (EC 3.4.25.1) (PROTEASOME THETA CHAIN) (PROTEASOME CHAIN 13) (PROTEASOME COMPONENT C10-II). [SWISSPROT;Acc:P49720] PSMB3 3.13091 0.249618801
0.784986 1591 BYSTIN. [SWISSPROT;Acc:Q13895] BYSL 3.26689 0.240285409
0.788413 49 FERRITIN HEAVY CHAIN (FERRITIN H SUBUNIT). [SWISSPROT;Acc:P02794] FTH1 1.91686 0.411304425
0.788679 1814 60S RIBOSOMAL PROTEIN L9. [SWISSPROT;Acc:P32969] no value 3.36493 0.234381993
0.788778 85 TRANSCRIPTION FACTOR DP-1 (E2F DIMERIZATION PARTNER 1) (DRTF1- POLYPEPTIDE-1) (DRTF1). [SWISSPROT;Acc:Q14186] 2.02915 0.388723357
0.790323 1639 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 7 (26S PROTEASOME REGULATORY SUBUNIT S12) (PROTEASOME SUBUNIT P40) (MOV34 PROTEIN HOMOLOG). [SWISSPROT;Acc:P51665] PSMD7 3.30538 0.239102009
0.790808 1 PROTEIN CGI-126 (PROTEIN HSPC155). [SWISSPROT;Acc:Q9Y3C8] UFC1 0.682179 1.159238264
0.795875 120 PONSIN; SH3-DOMAIN PROTEIN 5 (PONSIN). [RefSeq;Acc:NM_015385] SORBS1 2.20689 0.36063193
0.797221 1773 "RIBOSOMAL PROTEIN P0-LIKE PROTEIN; 60S ACIDIC RIBOSOMAL PROTEIN PO; RIBOSOMAL PROTEIN, LARGE, P0-LIKE. [RefSeq;Acc:NM_016183]" MRTO4 3.37861 0.235961238
0.801671 2865 PROBABLE ATP-DEPENDENT RNA HELICASE P54 (ONCOGENE RCK) (DEAD-BOX PROTEIN 6). [SWISSPROT;Acc:P26196] DDX6 4.24298 0.188940556
0.802935 379 CROOKED NECK-LIKE PROTEIN 1 (CROOKED NECK HOMOLOG) (HCRN) (CGI-201) (MSTP021). [SWISSPROT;Acc:Q9BZJ0] CRNKL1 2.8765 0.279136103
0.803534 9 DNA POLYMERASE EPSILON P12 SUBUNIT (DNA POLYMERASE EPSILON SUBUNIT 4). [SWISSPROT;Acc:Q9NR33] POLE4 1.40271 0.572843995
0.804341 2345 "PYRUVATE DEHYDROGENASE E1 COMPONENT BETA SUBUNIT, MITOCHONDRIAL PRECURSOR (EC 1.2.4.1) (PDHE1-B). [SWISSPROT;Acc:P11177]" PDHB 3.6465 0.220578911
0.804734 249 NASCENT-POLYPEPTIDE-ASSOCIATED COMPLEX ALPHA POLYPEPTIDE. [RefSeq;Acc:NM_005594] no value 2.57998 0.311914821
0.809232 184 LUC7-LIKE; SARCOPLASMIC RETICULUM PROTEIN LUC7B1. [RefSeq;Acc:NM_018032] LUC7L 2.44101 0.331515233
0.813157 1826 PROTEASOME SUBUNIT ALPHA TYPE 7 (EC 3.4.25.1) (PROTEASOME SUBUNIT RC6-1) (PROTEASOME SUBUNIT XAPC7). [SWISSPROT;Acc:O14818] PSMA7 3.47138 0.234246035
0.813888 11 XPA BINDING PROTEIN 1; MBD2 INTERACTOR PROTEIN; PUTATIVE ATP(GTP)-BINDING PROTEIN. [RefSeq;Acc:NM_007266] XAB1 1.5 0.542592
0.819252 174 U1 SMALL NUCLEAR RIBONUCLEOPROTEIN 70 KDA (U1 SNRNP 70 KDA) (SNRNP70) (U1-70K). [SWISSPROT;Acc:P08621] SNRP70 2.42854 0.337343424
0.820741 1951 DNA-DIRECTED RNA POLYMERASE I 135 KDA POLYPEPTIDE (EC 2.7.7.6) (RNA POLYMERASE I SUBUNIT 2) (RPA135). [SWISSPROT;Acc:Q9H9Y6] POLR1B 3.54858 0.231287163
0.824134 1820 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 8 (26S PROTEASOME REGULATORY SUBUNIT S14) (P31). [SWISSPROT;Acc:P48556] PSMD8 3.51793 0.234266742
0.825694 1872 26S PROTEASE REGULATORY SUBUNIT 4 (P26S4). [SWISSPROT;Acc:Q03527] PSMC1 3.54636 0.23282859
0.829705 1327 WD-REPEAT PROTEIN 12 (YTM1 HOMOLOG). [SWISSPROT;Acc:Q9GZL7] WDR12 3.37944 0.245515529
0.83123 1710 60S RIBOSOMAL PROTEIN L4 (L1). [SWISSPROT;Acc:P36578] RPL4 3.49797 0.237632112
0.832577 1073 EIF2AK4 3.30018 0.2522823
0.834926 2005 40S RIBOSOMAL PROTEIN S20. [SWISSPROT;Acc:P17075] RPS20 3.6186 0.230731775
0.839834 2852 SMALL GLUTAMINE RICH PROTEIN WITH TETRATRICOPEPTIDE REPEATS 2. [RefSeq;Acc:NM_019072] no value 4.39067 0.191276958
0.844333 1605 PROTEIN BAP28. [SWISSPROT;Acc:Q9H583] HEATR1 3.51976 0.239883685
0.844424 2550 "[PYRUVATE DEHYDROGENASE [LIPOAMIDE]] KINASE ISOZYME 1, MITOCHONDRIAL PRECURSOR (EC 2.7.1.99) (PYRUVATE DEHYDROGENASE KINASE ISOFORM 1). [SWISSPROT;Acc:Q15118]" PDK1 3.93515 0.214584959
0.84511 259 "EUKARYOTIC TRANSLATION INITIATION FACTOR 4 GAMMA, 3. [RefSeq;Acc:NM_003760]" EIF4G3 2.7378 0.308682154
0.845658 2549 "[PYRUVATE DEHYDROGENASE [LIPOAMIDE]] KINASE ISOZYME 2, MITOCHONDRIAL PRECURSOR (EC 2.7.1.99) (PYRUVATE DEHYDROGENASE KINASE ISOFORM 2). [SWISSPROT;Acc:Q15119]" PDK2 3.9409 0.214584993
0.845995 840 FEM-1 HOMOLOG B; FEM-1-LIKE DEATH RECEPTOR BINDING PROTEIN; FEM-1 (C.ELEGANS) HOMOLOG B. [RefSeq;Acc:NM_015322] FEM1B 3.24503 0.260704832
0.847098 1673 IMP3 3.55339 0.238391508
0.848404 2282 DNA-DIRECTED RNA POLYMERASE II 14.4 KDA POLYPEPTIDE (EC 2.7.7.6) (RPB6) (RPB14.4) (RPABC2). [SWISSPROT;Acc:P41584] POLR2F 3.81401 0.222444094
0.848985 1707 26S PROTEASE REGULATORY SUBUNIT 6B (MIP224) (MB67 INTERACTING PROTEIN) (TAT-BINDING PROTEIN-7) (TBP-7). [SWISSPROT;Acc:P43686] PSMC4 3.57194 0.237681764
0.850503 1530 EUKARYOTIC TRANSLATION INITIATION FACTOR 6 (EIF-6) (B4 INTEGRIN INTERACTOR) (CAB) (P27(BBP)) (B(2)GCN HOMOLOG). [SWISSPROT;Acc:P56537] EIF6 3.51033 0.242285768
0.856237 265 EUKARYOTIC TRANSLATION INITIATION FACTOR 4 GAMMA (EIF-4-GAMMA) (EIF- 4G) (EIF4G) (P220). [SWISSPROT;Acc:Q04637] EIF4G1 2.77604 0.308438279
0.856366 1283 "NUCLEOSTEMIN; PUTATIVE NUCLEOTIDE BINDING PROTEIN, ESTRADIOL-INDUCED. [RefSeq;Acc:NM_014366]" GNL3 3.47989 0.246089963
0.858096 1419 ATP-DEPENDENT RNA HELICASE DDX18 (DEAD-BOX PROTEIN 18) (MYC-REGULATED DEAD-BOX PROTEIN) (MRDB). [SWISSPROT;Acc:Q9NVP1] DDX18 3.51778 0.243931116

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/