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 expected measured final Hugo
Results: HTML CSV LaTeX Showing element 2458 to 2507 of 3206 in total
Rank
description
expected
measured
final
Hugo
2458 2.60988 0.565608 0.21671801 OXSM
2459 0.125575 0.027214 0.21671511 C20orf80
2460 BROMODOMAIN CONTAINING 7; BROMODOMAIN PROTEIN; BROMODOMAIN-CONTAINING 7. [RefSeq;Acc:NM_013263] 1.22885 0.26631 0.216714815 BRD7
2461 0.155511 0.0337015 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] 1.94413 0.42132 0.216713903 TADA2L
2465 0.970087 0.210228 0.21671046 BRD9
2466 GALECTIN-4 (LACTOSE-BINDING LECTIN 4) (L-36 LACTOSE BINDING PROTEIN) (L36LBP) (ANTIGEN NY-CO-27). [SWISSPROT;Acc:P56470] 1.77366 0.384329 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] 1.48248 0.321097 0.21659449 RNASEH2A
2468 45 KDA CALCIUM-BINDING PROTEIN PRECURSOR (CAB45) (STROMAL CELL-DERIVED FACTOR 4) (SDF-4). [SWISSPROT;Acc:Q9BRK5] 0.340556 0.0737619 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] 0.533671 0.115589 0.216592245 EPB41L3
2472 0.646308 0.139984 0.216590233 CUEDC2
2473 PROTEIN 4.1 (BAND 4.1) (P4.1) (EPB4.1) (4.1R). [SWISSPROT;Acc:P11171] 0.415778 0.0900531 0.216589382 EPB41
2474 BAND 4.1-LIKE PROTEIN 2 (GENERALLY EXPRESSED PROTEIN 4.1) (4.1G). [SWISSPROT;Acc:O43491] 0.422875 0.0915902 0.216589299 EPB41L2
2475 BAND 4.1-LIKE PROTEIN 1 (NEURONAL PROTEIN 4.1) (4.1N). [SWISSPROT;Acc:Q9H4G0] 0.407281 0.0882127 0.216589284 EPB41L1
2476 0.270652 0.0586202 0.21658883 LSM14A
2477 SIMILAR TO TRNA SYNTHETASE CLASS II. [RefSeq;Acc:NM_152268] 0.946559 0.205001 0.216574984 PARS2
2478 GALECTIN-9 (HOM-HD-21) (ECALECTIN). [SWISSPROT;Acc:O00182] 2.41413 0.522708 0.216520237 LGALS9
2479 PRE-MRNA CLEAVAGE COMPLEX II PROTEIN PCF11 (FRAGMENT). [SWISSPROT;Acc:O94913] 1.15996 0.251152 0.216517811 PCF11
2480 CHROMODOMAIN Y-LIKE PROTEIN 2. [RefSeq;Acc:NM_152342] 2.53881 0.549251 0.216341908 CDYL2
2481 TESTIS-SPECIFIC CHROMODOMAIN PROTEIN Y PROTEIN 2. [SWISSPROT;Acc:Q9Y6F7] 3.04797 0.659303 0.216308888 CDY2B
2482 TESTIS-SPECIFIC CHROMODOMAIN Y PROTEIN 1. [SWISSPROT;Acc:Q9Y6F8] 3.06866 0.663776 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] 1.59051 0.343973 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] 0.618915 0.13384 0.216249404 GPI
2486 CEREBRAL CELL ADHESION MOLECULE. [RefSeq;Acc:NM_016174] 0.719698 0.155588 0.216185122 CEECAM1
2487 0.768906 0.166202 0.21615386 GLT25D1
2488 FIBULIN-2 PRECURSOR. [SWISSPROT;Acc:P98095] 0.90295 0.195152 0.216127139 FBLN2
2489 0.898593 0.194172 0.216084479 no value
2490 XPMC2 PREVENTS MITOTIC CATASTROPHE 2 HOMOLOG; XENOPUS PREVENTS MITOTIC CATASTROPHE 2 HOMOLOG. [RefSeq;Acc:NM_020385] 0.801332 0.172887 0.215749527 REXO4
2491 DEHYDRODOLICHYL DIPHOSPHATE SYNTHASE. [RefSeq;Acc:NM_024887] 1.10654 0.238591 0.215618956 DHDDS
2492 1.11109 0.239571 0.215617997 no value
2493 SH3-CONTAINING GRB2-LIKE PROTEIN 3 (SH3 DOMAIN PROTEIN 2C) (EEN-B2). [SWISSPROT;Acc:Q99963] 0.795244 0.171407 0.215540136 SH3GL3
2494 METHIONYL-TRNA SYNTHETASE (EC 6.1.1.10) (METHIONINE--TRNA LIGASE) (METRS). [SWISSPROT;Acc:P56192] 0.297931 0.0641898 0.2154519 MARS
2495 HISTIDINE DECARBOXYLASE (EC 4.1.1.22) (HDC). [SWISSPROT;Acc:P19113] 0.402189 0.0866317 0.215400471 HDC
2496 ARMET PROTEIN PRECURSOR (ARGININE-RICH PROTEIN). [SWISSPROT;Acc:P55145] 0.403767 0.0869714 0.215399971 ARMET
2497 SH3-CONTAINING GRB2-LIKE PROTEIN 2 (SH3 DOMAIN PROTEIN 2A) (ENDOPHILIN 1) (EEN-B1). [SWISSPROT;Acc:Q99962] 0.735941 0.158519 0.215396343 SH3GL2
2498 "UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX CORE PROTEIN I, MITOCHONDRIAL PRECURSOR (EC 1.10.2.2). [SWISSPROT;Acc:P31930]" 0.776201 0.167149 0.215342418 UQCRC1
2499 "MITOCHONDRIAL PROCESSING PEPTIDASE ALPHA SUBUNIT, MITOCHONDRIAL PRECURSOR (EC 3.4.24.64) (ALPHA-MPP) (P-55) (HA1523). [SWISSPROT;Acc:Q10713]" 1.09378 0.235517 0.215323923 PMPCA
2500 "MITOCHONDRIAL PROCESSING PEPTIDASE BETA SUBUNIT, MITOCHONDRIAL PRECURSOR (EC 3.4.24.64) (BETA-MPP) (P-52). [SWISSPROT;Acc:O75439]" 0.969013 0.208649 0.215321157 PMPCB
2501 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] 0.800978 0.172401 0.215238121 SH3GL1
2502 KERATIN ASSOCIATED PROTEIN 9-4; KERATIN ASSOCIATED PROTEIN 9.4. [RefSeq;Acc:NM_033191] 4.7857 1.02862 0.214936164 no value
2503 JUNCTIONAL ADHESION MOLECULE 1 PRECURSOR (JAM) (PLATELET ADHESION MOLECULE 1) (PAM-1) (PLATELET F11 RECEPTOR). [SWISSPROT;Acc:Q9Y624] 1.23096 0.26445 0.214832326 F11R
2504 ORNITHINE DECARBOXYLASE ANTIZYME INHIBITOR. [SWISSPROT;Acc:O14977] 0.814661 0.174979 0.214787501 AZIN1
2505 ORNITHINE DECARBOXYLASE-LIKE PROTEIN (EC 4.1.1.17) (ODC-PARALOGUE) (ODC-P). [SWISSPROT;Acc:Q96A70] 0.827431 0.177719 0.214784073 ADC
2506 "PLECKSTRIN HOMOLOGY DOMAIN CONTAINING, FAMILY C (WITH FERM DOMAIN) MEMBER 1; MITOGEN INDUCIBLE 2; KINDLIN 2. [RefSeq;Acc:NM_006832]" 0.188688 0.0405241 0.214767765 PLEKHC1
2507 ALPHA-PARVIN (CALPONIN-LIKE INTEGRIN-LINKED KINASE BINDING PROTEIN) (CH-ILKBP). [SWISSPROT;Acc:Q9NVD7] no value

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/