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:
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Gene final expected Rank measured description Hugo
Results: HTML CSV LaTeX Showing element 702 to 751 of 3206 in total
final
expected
Rank
measured
description
Hugo
0.214784073 0.827431 2505 0.177719 ORNITHINE DECARBOXYLASE-LIKE PROTEIN (EC 4.1.1.17) (ODC-PARALOGUE) (ODC-P). [SWISSPROT;Acc:Q96A70] ADC
0.214787501 0.814661 2504 0.174979 ORNITHINE DECARBOXYLASE ANTIZYME INHIBITOR. [SWISSPROT;Acc:O14977] AZIN1
0.214832326 1.23096 2503 0.26445 JUNCTIONAL ADHESION MOLECULE 1 PRECURSOR (JAM) (PLATELET ADHESION MOLECULE 1) (PAM-1) (PLATELET F11 RECEPTOR). [SWISSPROT;Acc:Q9Y624] F11R
0.214936164 4.7857 2502 1.02862 KERATIN ASSOCIATED PROTEIN 9-4; KERATIN ASSOCIATED PROTEIN 9.4. [RefSeq;Acc:NM_033191] no value
0.215238121 0.800978 2501 0.172401 SH3-CONTAINING GRB2-LIKE PROTEIN 1 (SH3 DOMAIN PROTEIN 2B) (EXTRA ELEVEN-NINETEEN LEUKEMIA FUSION GENE) (EEN) (EEN FUSION PARTNER OF MLL). [SWISSPROT;Acc:Q99961] SH3GL1
0.215321157 0.969013 2500 0.208649 "MITOCHONDRIAL PROCESSING PEPTIDASE BETA SUBUNIT, MITOCHONDRIAL PRECURSOR (EC 3.4.24.64) (BETA-MPP) (P-52). [SWISSPROT;Acc:O75439]" PMPCB
0.215323923 1.09378 2499 0.235517 "MITOCHONDRIAL PROCESSING PEPTIDASE ALPHA SUBUNIT, MITOCHONDRIAL PRECURSOR (EC 3.4.24.64) (ALPHA-MPP) (P-55) (HA1523). [SWISSPROT;Acc:Q10713]" PMPCA
0.215342418 0.776201 2498 0.167149 "UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX CORE PROTEIN I, MITOCHONDRIAL PRECURSOR (EC 1.10.2.2). [SWISSPROT;Acc:P31930]" UQCRC1
0.215396343 0.735941 2497 0.158519 SH3-CONTAINING GRB2-LIKE PROTEIN 2 (SH3 DOMAIN PROTEIN 2A) (ENDOPHILIN 1) (EEN-B1). [SWISSPROT;Acc:Q99962] SH3GL2
0.215399971 0.403767 2496 0.0869714 ARMET PROTEIN PRECURSOR (ARGININE-RICH PROTEIN). [SWISSPROT;Acc:P55145] ARMET
0.215400471 0.402189 2495 0.0866317 HISTIDINE DECARBOXYLASE (EC 4.1.1.22) (HDC). [SWISSPROT;Acc:P19113] HDC
0.2154519 0.297931 2494 0.0641898 METHIONYL-TRNA SYNTHETASE (EC 6.1.1.10) (METHIONINE--TRNA LIGASE) (METRS). [SWISSPROT;Acc:P56192] MARS
0.215540136 0.795244 2493 0.171407 SH3-CONTAINING GRB2-LIKE PROTEIN 3 (SH3 DOMAIN PROTEIN 2C) (EEN-B2). [SWISSPROT;Acc:Q99963] SH3GL3
0.215617997 1.11109 2492 0.239571 no value
0.215618956 1.10654 2491 0.238591 DEHYDRODOLICHYL DIPHOSPHATE SYNTHASE. [RefSeq;Acc:NM_024887] DHDDS
0.215749527 0.801332 2490 0.172887 XPMC2 PREVENTS MITOTIC CATASTROPHE 2 HOMOLOG; XENOPUS PREVENTS MITOTIC CATASTROPHE 2 HOMOLOG. [RefSeq;Acc:NM_020385] REXO4
0.216084479 0.898593 2489 0.194172 no value
0.216127139 0.90295 2488 0.195152 FIBULIN-2 PRECURSOR. [SWISSPROT;Acc:P98095] FBLN2
0.21615386 0.768906 2487 0.166202 GLT25D1
0.216185122 0.719698 2486 0.155588 CEREBRAL CELL ADHESION MOLECULE. [RefSeq;Acc:NM_016174] CEECAM1
0.216249404 0.618915 2485 0.13384 GLUCOSE-6-PHOSPHATE ISOMERASE (EC 5.3.1.9) (GPI) (PHOSPHOGLUCOSE ISOMERASE) (PGI) (PHOSPHOHEXOSE ISOMERASE) (PHI) (NEUROLEUKIN) (NLK) (SPERM ANTIGEN-36) (SA-36). [SWISSPROT;Acc:P06744] GPI
0.216265852 1.59051 2484 0.343973 HEMK PROTEIN HOMOLOG (EC 2.1.1.-) (M.HSAHEMKP). [SWISSPROT;Acc:Q9Y5R4] HEMK1
0.216308095 3.06866 2482 0.663776 TESTIS-SPECIFIC CHROMODOMAIN Y PROTEIN 1. [SWISSPROT;Acc:Q9Y6F8] CDY1B
2483 "CHROMODOMAIN PROTEIN, Y CHROMOSOME-LIKE ISOFORM A; CDY-LIKE, AUTOSOMAL; TESTIS-SPECIFIC CHROMODOMAIN Y-LIKE PROTEIN. [RefSeq;Acc:NM_004824]" CDYL
0.216308888 3.04797 2481 0.659303 TESTIS-SPECIFIC CHROMODOMAIN PROTEIN Y PROTEIN 2. [SWISSPROT;Acc:Q9Y6F7] CDY2B
0.216341908 2.53881 2480 0.549251 CHROMODOMAIN Y-LIKE PROTEIN 2. [RefSeq;Acc:NM_152342] CDYL2
0.216517811 1.15996 2479 0.251152 PRE-MRNA CLEAVAGE COMPLEX II PROTEIN PCF11 (FRAGMENT). [SWISSPROT;Acc:O94913] PCF11
0.216520237 2.41413 2478 0.522708 GALECTIN-9 (HOM-HD-21) (ECALECTIN). [SWISSPROT;Acc:O00182] LGALS9
0.216574984 0.946559 2477 0.205001 SIMILAR TO TRNA SYNTHETASE CLASS II. [RefSeq;Acc:NM_152268] PARS2
0.21658883 0.270652 2476 0.0586202 LSM14A
0.216589284 0.407281 2475 0.0882127 BAND 4.1-LIKE PROTEIN 1 (NEURONAL PROTEIN 4.1) (4.1N). [SWISSPROT;Acc:Q9H4G0] EPB41L1
0.216589299 0.422875 2474 0.0915902 BAND 4.1-LIKE PROTEIN 2 (GENERALLY EXPRESSED PROTEIN 4.1) (4.1G). [SWISSPROT;Acc:O43491] EPB41L2
0.216589382 0.415778 2473 0.0900531 PROTEIN 4.1 (BAND 4.1) (P4.1) (EPB4.1) (4.1R). [SWISSPROT;Acc:P11171] EPB41
0.216590233 0.646308 2472 0.139984 CUEDC2
0.216592245 0.533671 2471 0.115589 BAND 4.1-LIKE PROTEIN 3 (4.1B) (DIFFERENTIALLY EXPRESSED IN ADENOCARCINOMA OF THE LUNG PROTEIN 1) (DAL-1). [SWISSPROT;Acc:Q9Y2J2] EPB41L3
0.216592572 0.340556 2468 0.0737619 45 KDA CALCIUM-BINDING PROTEIN PRECURSOR (CAB45) (STROMAL CELL-DERIVED FACTOR 4) (SDF-4). [SWISSPROT;Acc:Q9BRK5] SDF4
2469 "SPECTRIN BETA CHAIN, BRAIN 4 (SPECTRIN, NON-ERYTHROID BETA CHAIN 4) (BETA-V SPECTRIN) (BSPECV). [SWISSPROT;Acc:Q9NRC6]" SPTBN5
2470 LSM14B
0.21659449 1.48248 2467 0.321097 RIBONUCLEASE HI LARGE SUBUNIT (EC 3.1.26.-) (RNASE HI LARGE SUBUNIT) (RNASE H(35)) (RIBONUCLEASE H2) (RNASE H2). [SWISSPROT;Acc:O75792] RNASEH2A
0.216686964 1.77366 2466 0.384329 GALECTIN-4 (LACTOSE-BINDING LECTIN 4) (L-36 LACTOSE BINDING PROTEIN) (L36LBP) (ANTIGEN NY-CO-27). [SWISSPROT;Acc:P56470] LGALS4
0.21671046 0.970087 2465 0.210228 BRD9
0.216713903 1.94413 2464 0.42132 TRANSCRIPTIONAL ADAPTER 2-LIKE (ADA2-LIKE PROTEIN) (KL04P). [SWISSPROT;Acc:O75478] TADA2L
0.216714573 0.155511 2461 0.0337015 RPAP1
2462 FRG1 PROTEIN (FSHD REGION GENE 1 PROTEIN). [SWISSPROT;Acc:Q14331] FRG1
2463 TRANSCRIPTIONAL ADAPTOR 3-LIKE ISOFORM A. [RefSeq;Acc:NM_006354] TADA3L
0.216714815 1.22885 2460 0.26631 BROMODOMAIN CONTAINING 7; BROMODOMAIN PROTEIN; BROMODOMAIN-CONTAINING 7. [RefSeq;Acc:NM_013263] BRD7
0.21671511 0.125575 2459 0.027214 C20orf80
0.21671801 2.60988 2458 0.565608 OXSM
0.216721134 0.125458 2457 0.0271894 ZINC FINGER HOMEOBOX PROTEIN 1B (SMAD INTERACTING PROTEIN 1) (SMADIP1) (HRIHFB2411). [SWISSPROT;Acc:O60315] ZEB2
0.216721904 0.15207 2456 0.0329569 TRANSCRIPTION FACTOR 8 (NIL-2-A ZINC FINGER PROTEIN) (NEGATIVE REGULATOR OF IL2). [SWISSPROT;Acc:P37275] ZEB1

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/