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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Rank Gene description measured expected final Hugo
Results: HTML CSV LaTeX Showing element 151 to 200 of 350 in total
Hugo  : no value
Rank
description
measured
expected
final
1504 GUANINE NUCLEOTIDE-BINDING PROTEIN BETA SUBUNIT-LIKE PROTEIN 12.3 (P205) (RECEPTOR OF ACTIVATED PROTEIN KINASE C 1) (RACK1) (RECEPTOR FOR ACTIVATED C KINASE). [SWISSPROT;Acc:P25388] 0.112103 0.461933 0.24268238
1539 HISTONE H3.3 (H3.A) (H3.B) (H3.3Q). [SWISSPROT;Acc:P06351] 0.21933 0.906671 0.241906932
1540 DJ1099D15.1 (PUTATIVE DNAJ PROTEIN). [SPTREMBL;Acc:Q9H4J9] 0.0214576 0.0887019 0.241906881
1550 ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 7 (ADP-RIBOSYLATION FACTOR-LIKE PROTEIN LAK). [SWISSPROT;Acc:P56559] 0.0364961 0.150941 0.241790501
1556 0.184977 0.766628 0.241286517
1557 0.0753661 0.312352 0.241285793
1567 NEFA-INTERACTING NUCLEAR PROTEIN NIP30. [RefSeq;Acc:NM_024946] 0.0394801 0.163824 0.240990941
1584 HURPIN (HACAT UV-REPRESSIBLE SERPIN) (PROTEASE INHIBITOR 13) (HEADPIN) (SERPIN B13). [SWISSPROT;Acc:Q9UIV8] 0.0653411 0.271247 0.240891512
1600 TRANSLIN. [SWISSPROT;Acc:Q15631] 0.218752 0.911432 0.240009128
1642 0.0488461 0.204356 0.239024545
1646 MYOSIN VI. [SWISSPROT;Acc:Q9UM54] 0.050323 0.210535 0.23902439
1647 0.0275762 0.11537 0.23902401
1668 MESODERM INDUCTION EARLY RESPONSE 1. [RefSeq;Acc:NM_020948] 0.0415385 0.173966 0.238773668
1680 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 12 (26S PROTEASOME REGULATORY SUBUNIT P55). [SWISSPROT;Acc:O00232] 0.563839 2.36701 0.238207274
1683 NUCLEOLAR PROTEIN NOP5 (NUCLEOLAR PROTEIN 5) (NOP58) (HSPC120). [SWISSPROT;Acc:Q9Y2X3] 0.160247 0.672842 0.238164383
1700 0.044904 0.188793 0.237847802
1704 DJ408B20.3 (NOVEL PROTEIN SIMILAR TO 60S ACIDIC RIBOSOMAL PROTEIN P2 (RPLP2)). [SPTREMBL;Acc:Q9H5A9] 0.0573148 0.241075 0.237746759
1731 0.02137 0.0901539 0.237039108
1743 40S RIBOSOMAL PROTEIN S28. [SWISSPROT;Acc:P25112] 0.229236 0.968071 0.236796681
1751 VACUOLAR ATP SYNTHASE SUBUNIT G 2 (EC 3.6.3.14) (V-ATPASE G SUBUNIT 2) (VACUOLAR PROTON PUMP G SUBUNIT 2) (V-ATPASE 13 KDA SUBUNIT 2). [SWISSPROT;Acc:O95670] 0.0861167 0.363797 0.236716356
1764 0.0607427 0.257167 0.236199435
1766 "DJ850E9.1 (NOVEL C2H2 TYPE ZINC FINGER PROTEIN SIMILAR TO DROSOPHILA SCRATCH (SCRT), SLUG AND XENOPUS SNAIL) (FRAGMENT). [SPTREMBL;Acc:Q9NQ03]" 0.281698 1.1936 0.236007038
1772 HEAT SHOCK 70 KDA PROTEIN 1 (HSP70.1) (HSP70-1/HSP70-2). [SWISSPROT;Acc:P08107] 0.0654179 0.277203 0.235992756
1775 SCRATCH; SCRATCH 1. [RefSeq;Acc:NM_031309] 0.322861 1.36866 0.235895694
1780 ADENINE PHOSPHORIBOSYLTRANSFERASE (EC 2.4.2.7) (APRT). [SWISSPROT;Acc:P07741] 0.273997 1.16418 0.235356216
1782 17 BETA-HYDROXYSTEROID DEHYDROGENASE. [SPTREMBL;Acc:Q13034] 0.024834 0.105517 0.23535544
1800 0.0580492 0.247338 0.234695841
1814 60S RIBOSOMAL PROTEIN L9. [SWISSPROT;Acc:P32969] 0.788679 3.36493 0.234381993
1823 0.038359 0.163741 0.234266311
1841 60S RIBOSOMAL PROTEIN L39. [SWISSPROT;Acc:P02404] 0.187564 0.803133 0.233540397
1844 60S RIBOSOMAL PROTEIN L18A. [SWISSPROT;Acc:Q02543] 0.214359 0.917867 0.233540371
1852 PRESENILIN-LIKE PROTEIN 1 (EC 3.4.99.-) (SPPL2B PROTEIN). [SWISSPROT;Acc:Q8TCT7] 0.0331615 0.142049 0.233451133
1853
1854 0.0274494 0.117581 0.233450983
1855 PRESENILIN-LIKE PROTEIN 2 (EC 3.4.99.-) (SPPL2A PROTEIN). [SWISSPROT;Acc:Q8TCT8] 0.0275157 0.117865 0.233450982
1882 "CREATINE KINASE, UBIQUITOUS MITOCHONDRIAL PRECURSOR (EC 2.7.3.2) (U- MTCK) (MIA-CK) (ACIDIC-TYPE MITOCHONDRIAL CREATINE KINASE). [SWISSPROT;Acc:P12532]" 0.199469 0.856983 0.232757243
1889 DIHYDROFOLATE REDUCTASE (EC 1.5.1.3). [SWISSPROT;Acc:P00374] 0.241532 1.03785 0.232723419
1899 60S RIBOSOMAL PROTEIN L17 (L23). [SWISSPROT;Acc:P18621] 0.63284 2.72242 0.232454948
1902 0.549308 2.36366 0.232397214
1906 SUPPRESSOR OF TY 5 HOMOLOG; SUPPRESSOR OF TY (S.CEREVISIAE) 5 HOMOLOG. [RefSeq;Acc:NM_003169] 1.04135 4.48455 0.23220836
1913 HISTONE H4. [SWISSPROT;Acc:P02304] 0.0828779 0.35711 0.232079471
1916 BIFUNCTIONAL 3'-PHOSPHOADENOSINE 5'-PHOSPHOSULFATE SYNTHETHASE 2 (PAPS SYNTHETHASE 2) (PAPSS 2) (SULFURYLASE KINASE 2) (SK2) (SK 2) [INCLUDES: SULFATE ADENYLYLTRANSFERASE (EC 2.7.7.4) (SULFATE ADENYLATE TRANSFERASE) (SAT) (ATP-SULFURYLASE); ADENYLYLSULFAT 0.0174991 0.0754368 0.231970338
1928 0.704795 3.04081 0.231778704
1929 MULTISYNTHETASE COMPLEX AUXILIARY COMPONENT P38 (JTV-1 PROTEIN) (PRO0992). [SWISSPROT;Acc:Q13155] 0.122792 0.529927 0.231714934
1934 60S RIBOSOMAL PROTEIN L23A. [SWISSPROT;Acc:P29316] 1.40328 6.05655 0.231696263
1935 C367G8.3 (NOVEL PROTEIN SIMILAR TO RPL23A (60S RIBOSOMAL PROTEIN L23A)) (60S RIBOSOMAL PROTEIN L23A LIKE). [SPTREMBL;Acc:Q9BR02] 1.24769 5.38515 0.231690854
1937 U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM7. [SWISSPROT;Acc:Q9UK45] 0.268923 1.1607 0.231690359
1940 "ISOLEUCYL-TRNA SYNTHETASE, CYTOPLASMIC (EC 6.1.1.5) (ISOLEUCINE--TRNA LIGASE) (ILERS) (IRS). [SWISSPROT;Acc:P41252]" 0.0589414 0.254478 0.231616878
1943 40S RIBOSOMAL PROTEIN S15 (RIG PROTEIN). [SWISSPROT;Acc:P11174] 1.32362 5.71513 0.231599281
1953 60S RIBOSOMAL PROTEIN L14 (CAG-ISL 7). [SWISSPROT;Acc:P50914] 0.0571361 0.247068 0.231256577

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/