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:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene description measured expected final Hugo
Results: HTML CSV LaTeX Showing element 2451 to 2500 of 3206 in total
Rank
description
measured
expected
final
Hugo
2451 E-1 ENZYME. [RefSeq;Acc:NM_021204] 0.175357 0.808504 0.216890702 ENOPH1
2452 T-BOX TRANSCRIPTION FACTOR TBX19 (T-BOX PROTEIN 19). [SWISSPROT;Acc:O60806] 0.0222862 0.102768 0.216859334 TBX19
2453 BRACHYURY PROTEIN (T PROTEIN). [SWISSPROT;Acc:O15178] 0.0274799 0.126718 0.216858694 T
2454 0.278378 1.28369 0.216857653 REXO1
2455 REGULATOR OF CHROMOSOME CONDENSATION (CELL CYCLE REGULATORY PROTEIN). [SWISSPROT;Acc:P18754] 0.118612 0.5473 0.21672209 RCC1
2456 TRANSCRIPTION FACTOR 8 (NIL-2-A ZINC FINGER PROTEIN) (NEGATIVE REGULATOR OF IL2). [SWISSPROT;Acc:P37275] 0.0329569 0.15207 0.216721904 ZEB1
2457 ZINC FINGER HOMEOBOX PROTEIN 1B (SMAD INTERACTING PROTEIN 1) (SMADIP1) (HRIHFB2411). [SWISSPROT;Acc:O60315] 0.0271894 0.125458 0.216721134 ZEB2
2458 0.565608 2.60988 0.21671801 OXSM
2459 0.027214 0.125575 0.21671511 C20orf80
2460 BROMODOMAIN CONTAINING 7; BROMODOMAIN PROTEIN; BROMODOMAIN-CONTAINING 7. [RefSeq;Acc:NM_013263] 0.26631 1.22885 0.216714815 BRD7
2461 0.0337015 0.155511 0.216714573 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
2464 TRANSCRIPTIONAL ADAPTER 2-LIKE (ADA2-LIKE PROTEIN) (KL04P). [SWISSPROT;Acc:O75478] 0.42132 1.94413 0.216713903 TADA2L
2465 0.210228 0.970087 0.21671046 BRD9
2466 GALECTIN-4 (LACTOSE-BINDING LECTIN 4) (L-36 LACTOSE BINDING PROTEIN) (L36LBP) (ANTIGEN NY-CO-27). [SWISSPROT;Acc:P56470] 0.384329 1.77366 0.216686964 LGALS4
2467 RIBONUCLEASE HI LARGE SUBUNIT (EC 3.1.26.-) (RNASE HI LARGE SUBUNIT) (RNASE H(35)) (RIBONUCLEASE H2) (RNASE H2). [SWISSPROT;Acc:O75792] 0.321097 1.48248 0.21659449 RNASEH2A
2468 45 KDA CALCIUM-BINDING PROTEIN PRECURSOR (CAB45) (STROMAL CELL-DERIVED FACTOR 4) (SDF-4). [SWISSPROT;Acc:Q9BRK5] 0.0737619 0.340556 0.216592572 SDF4
2469 "SPECTRIN BETA CHAIN, BRAIN 4 (SPECTRIN, NON-ERYTHROID BETA CHAIN 4) (BETA-V SPECTRIN) (BSPECV). [SWISSPROT;Acc:Q9NRC6]" SPTBN5
2470 LSM14B
2471 BAND 4.1-LIKE PROTEIN 3 (4.1B) (DIFFERENTIALLY EXPRESSED IN ADENOCARCINOMA OF THE LUNG PROTEIN 1) (DAL-1). [SWISSPROT;Acc:Q9Y2J2] 0.115589 0.533671 0.216592245 EPB41L3
2472 0.139984 0.646308 0.216590233 CUEDC2
2473 PROTEIN 4.1 (BAND 4.1) (P4.1) (EPB4.1) (4.1R). [SWISSPROT;Acc:P11171] 0.0900531 0.415778 0.216589382 EPB41
2474 BAND 4.1-LIKE PROTEIN 2 (GENERALLY EXPRESSED PROTEIN 4.1) (4.1G). [SWISSPROT;Acc:O43491] 0.0915902 0.422875 0.216589299 EPB41L2
2475 BAND 4.1-LIKE PROTEIN 1 (NEURONAL PROTEIN 4.1) (4.1N). [SWISSPROT;Acc:Q9H4G0] 0.0882127 0.407281 0.216589284 EPB41L1
2476 0.0586202 0.270652 0.21658883 LSM14A
2477 SIMILAR TO TRNA SYNTHETASE CLASS II. [RefSeq;Acc:NM_152268] 0.205001 0.946559 0.216574984 PARS2
2478 GALECTIN-9 (HOM-HD-21) (ECALECTIN). [SWISSPROT;Acc:O00182] 0.522708 2.41413 0.216520237 LGALS9
2479 PRE-MRNA CLEAVAGE COMPLEX II PROTEIN PCF11 (FRAGMENT). [SWISSPROT;Acc:O94913] 0.251152 1.15996 0.216517811 PCF11
2480 CHROMODOMAIN Y-LIKE PROTEIN 2. [RefSeq;Acc:NM_152342] 0.549251 2.53881 0.216341908 CDYL2
2481 TESTIS-SPECIFIC CHROMODOMAIN PROTEIN Y PROTEIN 2. [SWISSPROT;Acc:Q9Y6F7] 0.659303 3.04797 0.216308888 CDY2B
2482 TESTIS-SPECIFIC CHROMODOMAIN Y PROTEIN 1. [SWISSPROT;Acc:Q9Y6F8] 0.663776 3.06866 0.216308095 CDY1B
2483 "CHROMODOMAIN PROTEIN, Y CHROMOSOME-LIKE ISOFORM A; CDY-LIKE, AUTOSOMAL; TESTIS-SPECIFIC CHROMODOMAIN Y-LIKE PROTEIN. [RefSeq;Acc:NM_004824]" CDYL
2484 HEMK PROTEIN HOMOLOG (EC 2.1.1.-) (M.HSAHEMKP). [SWISSPROT;Acc:Q9Y5R4] 0.343973 1.59051 0.216265852 HEMK1
2485 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] 0.13384 0.618915 0.216249404 GPI
2486 CEREBRAL CELL ADHESION MOLECULE. [RefSeq;Acc:NM_016174] 0.155588 0.719698 0.216185122 CEECAM1
2487 0.166202 0.768906 0.21615386 GLT25D1
2488 FIBULIN-2 PRECURSOR. [SWISSPROT;Acc:P98095] 0.195152 0.90295 0.216127139 FBLN2
2489 0.194172 0.898593 0.216084479 no value
2490 XPMC2 PREVENTS MITOTIC CATASTROPHE 2 HOMOLOG; XENOPUS PREVENTS MITOTIC CATASTROPHE 2 HOMOLOG. [RefSeq;Acc:NM_020385] 0.172887 0.801332 0.215749527 REXO4
2491 DEHYDRODOLICHYL DIPHOSPHATE SYNTHASE. [RefSeq;Acc:NM_024887] 0.238591 1.10654 0.215618956 DHDDS
2492 0.239571 1.11109 0.215617997 no value
2493 SH3-CONTAINING GRB2-LIKE PROTEIN 3 (SH3 DOMAIN PROTEIN 2C) (EEN-B2). [SWISSPROT;Acc:Q99963] 0.171407 0.795244 0.215540136 SH3GL3
2494 METHIONYL-TRNA SYNTHETASE (EC 6.1.1.10) (METHIONINE--TRNA LIGASE) (METRS). [SWISSPROT;Acc:P56192] 0.0641898 0.297931 0.2154519 MARS
2495 HISTIDINE DECARBOXYLASE (EC 4.1.1.22) (HDC). [SWISSPROT;Acc:P19113] 0.0866317 0.402189 0.215400471 HDC
2496 ARMET PROTEIN PRECURSOR (ARGININE-RICH PROTEIN). [SWISSPROT;Acc:P55145] 0.0869714 0.403767 0.215399971 ARMET
2497 SH3-CONTAINING GRB2-LIKE PROTEIN 2 (SH3 DOMAIN PROTEIN 2A) (ENDOPHILIN 1) (EEN-B1). [SWISSPROT;Acc:Q99962] 0.158519 0.735941 0.215396343 SH3GL2
2498 "UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX CORE PROTEIN I, MITOCHONDRIAL PRECURSOR (EC 1.10.2.2). [SWISSPROT;Acc:P31930]" 0.167149 0.776201 0.215342418 UQCRC1
2499 "MITOCHONDRIAL PROCESSING PEPTIDASE ALPHA SUBUNIT, MITOCHONDRIAL PRECURSOR (EC 3.4.24.64) (ALPHA-MPP) (P-55) (HA1523). [SWISSPROT;Acc:Q10713]" 0.235517 1.09378 0.215323923 PMPCA
2500 "MITOCHONDRIAL PROCESSING PEPTIDASE BETA SUBUNIT, MITOCHONDRIAL PRECURSOR (EC 3.4.24.64) (BETA-MPP) (P-52). [SWISSPROT;Acc:O75439]" 0.208649 0.969013 0.215321157 PMPCB

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/