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 Rank Gene Hugo description expected final
Results: HTML CSV LaTeX Showing element 152 to 201 of 3206 in total
measured
Rank
Hugo
description
expected
final
0.025126 2620 ESD ESTERASE D (EC 3.1.1.1). [SWISSPROT;Acc:P10768] 0.119364 0.210498978
0.0252114 2737 VAMP2 VESICLE-ASSOCIATED MEMBRANE PROTEIN 2 (VAMP-2) (SYNAPTOBREVIN 2). [SWISSPROT;Acc:P19065] 0.122785 0.205329641
2738 TMEM64
2739 VAMP4 VESICULE-ASSOCIATED MEMBRANE PROTEIN 4 (VAMP-4). [SWISSPROT;Acc:O75379]
0.0252117 1845 MRPL22 MITOCHONDRIAL RIBOSOMAL PROTEIN L22. [RefSeq;Acc:NM_014180] 0.107989 0.233465446
0.0252313 1857 FCF1 0.108089 0.233430784
0.0252512 2405 ITM2A INTEGRAL MEMBRANE PROTEIN 2A (E25 PROTEIN). [SWISSPROT;Acc:O43736] 0.115441 0.218736844
0.02527 2666 no value NEURAL CELL ADHESION MOLECULE L1 PRECURSOR (N-CAM L1) (CD171 ANTIGEN). [SWISSPROT;Acc:P32004] 0.120774 0.209233775
0.025294 819 MYL3 "MYOSIN LIGHT CHAIN 1, SLOW-TWITCH MUSCLE B/VENTRICULAR ISOFORM (MLC1SB) (ALKALI). [SWISSPROT;Acc:P08590]" 0.0967906 0.26132703
0.0253172 2904 SAP30 "SIN3 ASSOCIATED POLYPEPTIDE P30; SIN3-ASSOCIATED POLYPEPTIDE, 30KD. [RefSeq;Acc:NM_003864]" 0.145382 0.174142604
0.0253936 2601 VPS72 YL-1 PROTEIN (TRANSCRIPTION FACTOR-LIKE 1). [SWISSPROT;Acc:Q15906] 0.119307 0.212842499
0.0254221 2356 GLI1 ZINC FINGER PROTEIN GLI1 (GLIOMA-ASSOCIATED ONCOGENE) (ONCOGENE GLI). [SWISSPROT;Acc:P08151] 0.115399 0.220297403
2357 GLI2 ZINC FINGER PROTEIN GLI2 (TAX HELPER PROTEIN). [SWISSPROT;Acc:P10070]
0.0254237 1231 DDX31 DEAD (ASP-GLU-ALA-ASP) BOX POLYPEPTIDE 31 ISOFORM 1; DEAD/DEXH HELICASE DDX31. [RefSeq;Acc:NM_022779] 0.102605 0.247782272
0.0254509 2158 SPCS2 MICROSOMAL SIGNAL PEPTIDASE 25 KDA SUBUNIT (EC 3.4.-.-) (SPASE 25 KDA SUBUNIT) (SPC25). [SWISSPROT;Acc:Q15005] 0.111998 0.227244237
0.0255016 821 MYL1 "MYOSIN LIGHT CHAIN 1, SKELETAL MUSCLE ISOFORM (MLC1F) (A1 CATALYTIC) (ALKALI). [SWISSPROT;Acc:P05976]" 0.0975853 0.261326245
0.0255652 2593 SLC25A12 "CALCIUM-BINDING MITOCHONDRIAL CARRIER PROTEIN ARALAR1 (SOLUTE CARRIER FAMILY 25, MEMBER 12). [SWISSPROT;Acc:O75746]" 0.120086 0.212890762
0.0255653 2590 no value DC11 PROTEIN. [RefSeq;Acc:NM_020186] 0.212891594
2591 HHAT MELANOMA ANTIGEN RECOGNIZED BY T CELLS 2. [RefSeq;Acc:NM_018194]
2592 no value HEPATITIS C VIRUS CORE-BINDING PROTEIN 6; CERVICAL CANCER ONCOGENE 3. [RefSeq;Acc:NM_023934]
0.0255702 1443 COQ2 0.105024 0.243470064
0.0256005 1511 NGDN 0.105559 0.242523139
0.0256013 1528 NET1 NEUROEPITHELIAL CELL TRANSFORMING GENE 1; GUANINE NUCLEOTIDE REGULATORY PROTEIN (ONCOGENE); RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR (GEF) 8. [RefSeq;Acc:NM_005863] 0.105652 0.24231723
0.0256055 2406 ITM2C INTEGRAL MEMBRANE PROTEIN 2C (TRANSMEMBRANE PROTEIN BRI3) (NPD018). [SWISSPROT;Acc:Q9NQX7] 0.117061 0.218736385
0.0256535 1695 SLC25A31 0.107847 0.237869389
0.0256791 2118 DPY19L1 0.112542 0.228173482
0.0257019 485 CHCHD3 0.0936986 0.274303992
0.0257685 3183 PSEN2 PRESENILIN 2 (PS-2) (STM-2) (E5-1) (AD3LP) (AD5). [SWISSPROT;Acc:P49810] 0.517685 0.049776408
0.0257797 2417 SERINC1 TUMOR DIFFERENTIALLY EXPRESSED 1 PROTEIN LIKE. [SWISSPROT;Acc:Q9NRX5] 0.118068 0.218346207
0.0258082 1781 HSD17B1 ESTRADIOL 17 BETA-DEHYDROGENASE 1 (EC 1.1.1.62) (17-BETA-HSD 1) (PLACENTAL 17-BETA-HYDROXYSTEROID DEHYDROGENASE) (20 ALPHA- HYDROXYSTEROID DEHYDROGENASE) (20-ALPHA-HSD) (E2DH). [SWISSPROT;Acc:P14061] 0.109656 0.235356022
0.0258274 2612 ATP5J2 "ATP SYNTHASE F CHAIN, MITOCHONDRIAL (EC 3.6.3.14). [SWISSPROT;Acc:P56134]" 0.122212 0.211332766
2613 DHX35 PROBABLE ATP-DEPENDENT HELICASE DDX35 (DEAH-BOX PROTEIN 35). [SWISSPROT;Acc:Q9H5Z1]
0.0258656 2531 no value KERATIN ASSOCIATED PROTEIN 1-3; KERATIN ASSOCIATED PROTEIN 1.3. [RefSeq;Acc:NM_030966] 0.120439 0.214760999
0.0258973 2375 THIAMIN PYROPHOSPHOKINASE 1; MOUSE THIAMIN PYROPHOSPHOKINASE HOMOLOG; THIAMINE PYROPHOSPHOKINASE. [RefSeq;Acc:NM_022445] 0.117689 0.220048603
0.0259096 820 "MYOSIN LIGHT CHAIN 1, EMBRYONIC MUSCLE/ATRIAL ISOFORM (PRO1957). [SWISSPROT;Acc:P12829]" 0.0991465 0.261326421
0.0260119 1410 HS6ST2 HEPARAN SULFATE 6-O-SULFOTRANSFERASE 2. [RefSeq;Acc:NM_147174] 0.106604 0.244004915
0.0260682 2534 no value KERATIN ASSOCIATED PROTEIN 4.3 (FRAGMENT). [SPTREMBL;Acc:Q9BYR4] 0.121383 0.214759892
0.0261125 953 ABHD1 ALPHA/BETA HYDROLASE DOMAIN CONTAINING PROTEIN 1 ISOFORM 2; LUNG ALPHA/BETA HYDROLASE PROTEIN 1. [RefSeq;Acc:NM_152870] 0.101841 0.256404591
0.0263893 1414 FA2H FATTY ACID HYDROXYLASE DOMAIN CONTAINING 1. [RefSeq;Acc:NM_024306] 0.108151 0.244004216
0.02648 489 ZNF289 "ZINC FINGER PROTEIN 289, ID1 REGULATED; LIKELY ORTHOLOG OF MOUSE ZFP289. [RefSeq;Acc:NM_032389]" 0.0965355 0.274303236
0.0265832 883 PIK3C2B PHOSPHATIDYLINOSITOL-4-PHOSPHATE 3-KINASE C2 DOMAIN-CONTAINING BETA POLYPEPTIDE (EC 2.7.1.154) (PHOSPHOINOSITIDE 3-KINASE-C2-BETA) (PTDINS-3-KINASE C2 BETA) (PI3K-C2BETA) (C2-PI3K). [SWISSPROT;Acc:O00750] 0.102213 0.260076507
0.0266534 1305 P4HA2 "PROLYL 4-HYDROXYLASE ALPHA-2 SUBUNIT PRECURSOR (EC 1.14.11.2) (4-PH ALPHA-2) (PROCOLLAGEN-PROLINE,2-OXOGLUTARATE-4-DIOXYGENASE ALPHA-2 SUBUNIT). [SWISSPROT;Acc:O15460]" 0.108468 0.245725928
0.0267797 2270 NPEPPS PUROMYCIN-SENSITIVE AMINOPEPTIDASE (EC 3.4.11.-) (PSA). [SWISSPROT;Acc:P55786] 0.120229 0.222739106
0.0267948 1840 C18orf22 0.114733 0.233540481
0.0267969 1688 NEK3 SERINE/THREONINE-PROTEIN KINASE NEK3 (EC 2.7.1.37) (NIMA-RELATED PROTEIN KINASE 3) (HSPK 36). [SWISSPROT;Acc:P51956] 0.112547 0.238095196
0.026835 2992 HS3ST3A1 HEPARAN SULFATE D-GLUCOSAMINYL 3-O-SULFOTRANSFERASE 3A1; HEPARIN-GLUCOSAMINE 3-O-SULFOTRANSFERASE. [RefSeq;Acc:NM_006042] 0.198284 0.135336184
0.0268629 1381 GSK3A GLYCOGEN SYNTHASE KINASE-3 ALPHA (EC 2.7.1.37) (GSK-3 ALPHA). [SWISSPROT;Acc:P49840] 0.109803 0.244646321
0.0269837 769 COX4NB NEIGHBOR OF COX4. [SWISSPROT;Acc:O43402] 0.102351 0.263638851
0.0270059 1096 PGAM2 PHOSPHOGLYCERATE MUTASE 2 (EC 5.4.2.1) (EC 5.4.2.4) (EC 3.1.3.13) (PHOSPHOGLYCERATE MUTASE ISOZYME M) (PGAM-M) (BPG-DEPENDENT PGAM 2) (MUSCLE-SPECIFIC PHOSPHOGLYCERATE MUTASE). [SWISSPROT;Acc:P15259] 0.10746 0.251311186
0.027115 3197 VPS24 NEUROENDOCRINE DIFFERENTIATION FACTOR; COMPARATIVE GENE IDENTIFICATION TRANSCRIPT 149. [RefSeq;Acc:NM_016079] 0.735578 0.036862168

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/