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 Hugo Gene Rank description expected final
Results: HTML CSV LaTeX Showing element 208 to 257 of 3206 in total
measured
Hugo
Rank
description
expected
final
0.0273323 FAM86B2 2545 0.127356 0.214613367
0.0274232 TMOD4 2295 SKELETAL MUSCLE TROPOMODULIN (SK-TMOD) (TROPOMODULIN 4). [SWISSPROT;Acc:Q9NZQ9] 0.123338 0.222341857
0.027437 SUV39H1 2006 "HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-9 SPECIFIC 1 (EC 2.1.1.43) (HISTONE H3-K9 METHYLTRANSFERASE 1) (H3-K9-HMTASE 1) (SUPPRESSOR OF VARIEGATION 3-9 HOMOLOG 1) (SU(VAR)3-9 HOMOLOG 1). [SWISSPROT;Acc:O43463]" 0.118935 0.230689032
0.0274494 no value 1854 0.117581 0.233450983
0.0274568 POLG 2311 DNA POLYMERASE GAMMA SUBUNIT 1 (EC 2.7.7.7) (MITOCHONDRIAL DNA POLYMERASE CATALYTIC SUBUNIT) (POLG-ALPHA). [SWISSPROT;Acc:P54098] 0.123653 0.22204718
0.0274799 T 2453 BRACHYURY PROTEIN (T PROTEIN). [SWISSPROT;Acc:O15178] 0.126718 0.216858694
0.0274831 ADCK4 1653 AARF DOMAIN CONTAINING KINASE 4. [RefSeq;Acc:NM_024876] 0.115005 0.238973088
0.0275088 SLC37A1 913 GLYCEROL-3-PHOSPHATE TRANSPORTER (G-3-P TRANSPORTER) (G-3-P PERMEASE). [SWISSPROT;Acc:P57057] 0.106609 0.2580345
0.0275157 no value 1855 PRESENILIN-LIKE PROTEIN 2 (EC 3.4.99.-) (SPPL2A PROTEIN). [SWISSPROT;Acc:Q8TCT8] 0.117865 0.233450982
0.0275634 SDF2 1891 STROMAL CELL-DERIVED FACTOR 2 PRECURSOR (SDF-2). [SWISSPROT;Acc:Q99470] 0.118439 0.23272233
TYMS 1892 THYMIDYLATE SYNTHASE (EC 2.1.1.45) (TS) (TSASE). [SWISSPROT;Acc:P04818]
0.0275762 no value 1647 0.11537 0.23902401
0.0275767 LIPA 1851 LYSOSOMAL ACID LIPASE/CHOLESTERYL ESTER HYDROLASE PRECURSOR (EC 3.1.1.13) (LAL) (ACID CHOLESTERYL ESTER HYDROLASE) (STEROL ESTERASE) (LIPASE A) (CHOLESTERYL ESTERASE). [SWISSPROT;Acc:P38571] 0.118126 0.233451569
LIPF 1850 "TRIACYLGLYCEROL LIPASE, GASTRIC PRECURSOR (EC 3.1.1.3) (GASTRIC LIPASE) (GL). [SWISSPROT;Acc:P07098]"
0.0276089 TMOD3 2292 UBIQUITOUS TROPOMODULIN (U-TMOD) (TROPOMODULIN 3). [SWISSPROT;Acc:Q9NYL9] 0.124173 0.222342216
0.027794 GCLC 2743 GLUTAMATE--CYSTEINE LIGASE CATALYTIC SUBUNIT (EC 6.3.2.2) (GAMMA- GLUTAMYLCYSTEINE SYNTHETASE) (GAMMA-ECS) (GCS HEAVY CHAIN). [SWISSPROT;Acc:P48506] 0.135904 0.204512008
0.0279282 FAM98A 1933 0.120529 0.23171353
0.0279589 MCM3 1516 DNA REPLICATION LICENSING FACTOR MCM3 (DNA POLYMERASE ALPHA HOLOENZYME-ASSOCIATED PROTEIN P1) (RLF BETA SUBUNIT) (P102 PROTEIN) (P1-MCM3). [SWISSPROT;Acc:P25205] 0.115356 0.242370575
0.0280218 C14orf153 2385 0.127549 0.219694392
MOCS2 2386 MOLYBDENUM COFACTOR SYNTHESIS PROTEIN 2 LARGE SUBUNIT (MOLYBDOPTERIN SYNTHASE LARGE SUBUNIT) (MPT SYNTHASE LARGE SUBUNIT) (MOCS2B) (MOCO1- B). [SWISSPROT;Acc:O96007]
URM1 2387
0.0280741 no value 2529 KERATIN ASSOCIATED PROTEIN 4-10; KERATIN ASSOCIATED PROTEIN 4.10. [RefSeq;Acc:NM_033060] 0.130722 0.214761861
0.0280767 PDC 1058 PHOSDUCIN (PHD) (33 KDA PHOTOTRANSDUCING PROTEIN) (MEKA PROTEIN). [SWISSPROT;Acc:P20941] 0.11112 0.252670086
0.0281672 MSRA 2224 PEPTIDE METHIONINE SULFOXIDE REDUCTASE (EC 1.8.4.6) (PROTEIN- METHIONINE-S-OXIDE REDUCTASE) (PEPTIDE MET(O) REDUCTASE). [SWISSPROT;Acc:Q9UJ68] 0.125329 0.224746068
0.0281805 no value 1003 HUNTINGTIN INTERACTING PROTEIN E; HUNTINGTIN INTERACTOR PROTEIN E. [RefSeq;Acc:NM_007076] 0.110551 0.254909499
0.0281946 POLDIP2 1976 DNA POLYMERASE DELTA P38 SUBUNIT. [RefSeq;Acc:NM_015584] 0.122012 0.231080549
0.028203 CASP7 1830 CASPASE-7 PRECURSOR (EC 3.4.22.-) (ICE-LIKE APOPTOTIC PROTEASE 3) (ICE-LAP3) (APOPTOTIC PROTEASE MCH-3) (CMH-1). [SWISSPROT;Acc:P55210] 0.120482 0.23408476
0.0282774 IRX4 2142 IROQUOIS-CLASS HOMEODOMAIN PROTEIN IRX-4 (IROQUOIS HOMEOBOX PROTEIN 4). [SWISSPROT;Acc:P78413] 0.12412 0.227823074
ZC3H12A 2143
0.0283406 NUCB2 2210 NUCLEOBINDIN 2 PRECURSOR (DNA-BINDING PROTEIN NEFA). [SWISSPROT;Acc:P80303] 0.125928 0.225053999
0.0283438 SIN3A 2029 "TRANSCRIPTIONAL CO-REPRESSOR SIN3A; TRANSCRIPTIONAL REGULATOR, SIN3A (YEAST). [RefSeq;Acc:NM_015477]" 0.123075 0.230296973
0.0283513 GRM2 2557 METABOTROPIC GLUTAMATE RECEPTOR 2 PRECURSOR (MGLUR2). [SWISSPROT;Acc:Q14416] 0.132289 0.214313359
0.0283804 AURKC 1254 SERINE/THREONINE PROTEIN KINASE 13 (EC 2.7.1.37) (AURORA/IPL1/EG2 PROTEIN 2) (AURORA/IPL1-RELATED KINASE 3) (AURORA-C). [SWISSPROT;Acc:Q9UQB9] 0.114745 0.247334524
0.0284601 STT3A 2997 OLIGOSACCHARYL TRANSFERASE STT3 SUBUNIT HOMOLOG (B5) (INTEGRAL MEMBRANE PROTEIN 1) (TMC). [SWISSPROT;Acc:P46977] 0.210671 0.135092633
0.0285187 no value 659 SECRETED MODULAR CALCIUM-BINDING PROTEIN 1. [RefSeq;Acc:NM_022137] 0.106766 0.267114063
0.0285481 MARCH1 1881 0.122644 0.232772088
0.0285544 AURKB 1257 SERINE/THREONINE PROTEIN KINASE 12 (EC 2.7.1.37) (AURORA- AND IPL1- LIKE MIDBODY-ASSOCIATED PROTEIN 1) (AIM-1) (AURORA/IPL1-RELATED KINASE 2) (AURORA-RELATED KINASE 2) (STK-1) (AURORA-B). [SWISSPROT;Acc:Q96GD4] 0.115449 0.247333455
0.0286746 no value 504 ENIGMA PROTEIN; LIM DOMAIN PROTEIN. [RefSeq;Acc:NM_005451] 0.104626 0.274067631
0.0287078 CCT3 3170 "T-COMPLEX PROTEIN 1, GAMMA SUBUNIT (TCP-1-GAMMA) (CCT-GAMMA). [SWISSPROT;Acc:P49368]" 0.485319 0.059152434
0.0287655 TMEM91 2344 "2-OXOISOVALERATE DEHYDROGENASE ALPHA SUBUNIT, MITOCHONDRIAL PRECURSOR (EC 1.2.4.4) (BRANCHED-CHAIN ALPHA-KETO ACID DEHYDROGENASE E1 COMPONENT ALPHA CHAIN) (BCKDH E1-ALPHA). [SWISSPROT;Acc:P12694]" 0.130409 0.220579101
0.028817 no value 3187 "PROTEIN PHOSPHATASE 1, REGULATORY (INHIBITOR) SUBUNIT 14C; SEROLOGICALLY DEFINED BREAST CANCER ANTIGEN NY-BR-81; PKC-POTENTIATED PP1 INHIBITORY PROTEIN. [RefSeq;Acc:NM_030949]" 0.772261 0.037315105
0.0289077 ANLN 3202 "ANILLIN, ACTIN BINDING PROTEIN (SCRAPS HOMOLOG, DROSOPHILA); ANILLIN (DROSOPHILA SCRAPS HOMOLOG), ACTIN BINDING PROTEIN. [RefSeq;Acc:NM_018685]" 1.20992 0.023892241
0.0289523 TEX28P2 803 TESTIS-SPECIFIC PROTEIN TEX28. [SWISSPROT;Acc:O15482] 0.1105 0.262011765
0.0289586 KIAA1012 2742 TRS85 HOMOLOG. [SWISSPROT;Acc:Q9Y2L5] 0.141385 0.204820879
0.029 RRAGC 3201 RAS-RELATED GTP BINDING C; RAG C PROTEIN. [RefSeq;Acc:NM_022157] 1.21378 0.023892303
0.0290537 COQ10B 2054 0.126477 0.229715284
0.0291377 KIAA1033 2241 0.130208 0.223778109
0.0292681 DDX43 2972 DEAD-BOX PROTEIN. [RefSeq;Acc:NM_018665] 0.208597 0.140309305
TBCC 2971 TUBULIN-SPECIFIC CHAPERONE C (TUBULIN-FOLDING COFACTOR C) (CFC). [SWISSPROT;Acc:Q15814]
0.0293247 GNG11 3050 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(O) GAMMA-11 SUBUNIT. [SWISSPROT;Acc:P50152] 0.274937 0.106659707

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/