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 measured Gene description Hugo expected final
Results: HTML CSV LaTeX Showing element 2458 to 2507 of 3206 in total
Rank
measured
description
Hugo
expected
final
2458 0.565608 OXSM 2.60988 0.21671801
2459 0.027214 C20orf80 0.125575 0.21671511
2460 0.26631 BROMODOMAIN CONTAINING 7; BROMODOMAIN PROTEIN; BROMODOMAIN-CONTAINING 7. [RefSeq;Acc:NM_013263] BRD7 1.22885 0.216714815
2461 0.0337015 RPAP1 0.155511 0.216714573
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 0.42132 TRANSCRIPTIONAL ADAPTER 2-LIKE (ADA2-LIKE PROTEIN) (KL04P). [SWISSPROT;Acc:O75478] TADA2L 1.94413 0.216713903
2465 0.210228 BRD9 0.970087 0.21671046
2466 0.384329 GALECTIN-4 (LACTOSE-BINDING LECTIN 4) (L-36 LACTOSE BINDING PROTEIN) (L36LBP) (ANTIGEN NY-CO-27). [SWISSPROT;Acc:P56470] LGALS4 1.77366 0.216686964
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 1.48248 0.21659449
2468 0.0737619 45 KDA CALCIUM-BINDING PROTEIN PRECURSOR (CAB45) (STROMAL CELL-DERIVED FACTOR 4) (SDF-4). [SWISSPROT;Acc:Q9BRK5] SDF4 0.340556 0.216592572
2469 "SPECTRIN BETA CHAIN, BRAIN 4 (SPECTRIN, NON-ERYTHROID BETA CHAIN 4) (BETA-V SPECTRIN) (BSPECV). [SWISSPROT;Acc:Q9NRC6]" SPTBN5
2470 LSM14B
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 0.533671 0.216592245
2472 0.139984 CUEDC2 0.646308 0.216590233
2473 0.0900531 PROTEIN 4.1 (BAND 4.1) (P4.1) (EPB4.1) (4.1R). [SWISSPROT;Acc:P11171] EPB41 0.415778 0.216589382
2474 0.0915902 BAND 4.1-LIKE PROTEIN 2 (GENERALLY EXPRESSED PROTEIN 4.1) (4.1G). [SWISSPROT;Acc:O43491] EPB41L2 0.422875 0.216589299
2475 0.0882127 BAND 4.1-LIKE PROTEIN 1 (NEURONAL PROTEIN 4.1) (4.1N). [SWISSPROT;Acc:Q9H4G0] EPB41L1 0.407281 0.216589284
2476 0.0586202 LSM14A 0.270652 0.21658883
2477 0.205001 SIMILAR TO TRNA SYNTHETASE CLASS II. [RefSeq;Acc:NM_152268] PARS2 0.946559 0.216574984
2478 0.522708 GALECTIN-9 (HOM-HD-21) (ECALECTIN). [SWISSPROT;Acc:O00182] LGALS9 2.41413 0.216520237
2479 0.251152 PRE-MRNA CLEAVAGE COMPLEX II PROTEIN PCF11 (FRAGMENT). [SWISSPROT;Acc:O94913] PCF11 1.15996 0.216517811
2480 0.549251 CHROMODOMAIN Y-LIKE PROTEIN 2. [RefSeq;Acc:NM_152342] CDYL2 2.53881 0.216341908
2481 0.659303 TESTIS-SPECIFIC CHROMODOMAIN PROTEIN Y PROTEIN 2. [SWISSPROT;Acc:Q9Y6F7] CDY2B 3.04797 0.216308888
2482 0.663776 TESTIS-SPECIFIC CHROMODOMAIN Y PROTEIN 1. [SWISSPROT;Acc:Q9Y6F8] CDY1B 3.06866 0.216308095
2483 "CHROMODOMAIN PROTEIN, Y CHROMOSOME-LIKE ISOFORM A; CDY-LIKE, AUTOSOMAL; TESTIS-SPECIFIC CHROMODOMAIN Y-LIKE PROTEIN. [RefSeq;Acc:NM_004824]" CDYL
2484 0.343973 HEMK PROTEIN HOMOLOG (EC 2.1.1.-) (M.HSAHEMKP). [SWISSPROT;Acc:Q9Y5R4] HEMK1 1.59051 0.216265852
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 0.618915 0.216249404
2486 0.155588 CEREBRAL CELL ADHESION MOLECULE. [RefSeq;Acc:NM_016174] CEECAM1 0.719698 0.216185122
2487 0.166202 GLT25D1 0.768906 0.21615386
2488 0.195152 FIBULIN-2 PRECURSOR. [SWISSPROT;Acc:P98095] FBLN2 0.90295 0.216127139
2489 0.194172 no value 0.898593 0.216084479
2490 0.172887 XPMC2 PREVENTS MITOTIC CATASTROPHE 2 HOMOLOG; XENOPUS PREVENTS MITOTIC CATASTROPHE 2 HOMOLOG. [RefSeq;Acc:NM_020385] REXO4 0.801332 0.215749527
2491 0.238591 DEHYDRODOLICHYL DIPHOSPHATE SYNTHASE. [RefSeq;Acc:NM_024887] DHDDS 1.10654 0.215618956
2492 0.239571 no value 1.11109 0.215617997
2493 0.171407 SH3-CONTAINING GRB2-LIKE PROTEIN 3 (SH3 DOMAIN PROTEIN 2C) (EEN-B2). [SWISSPROT;Acc:Q99963] SH3GL3 0.795244 0.215540136
2494 0.0641898 METHIONYL-TRNA SYNTHETASE (EC 6.1.1.10) (METHIONINE--TRNA LIGASE) (METRS). [SWISSPROT;Acc:P56192] MARS 0.297931 0.2154519
2495 0.0866317 HISTIDINE DECARBOXYLASE (EC 4.1.1.22) (HDC). [SWISSPROT;Acc:P19113] HDC 0.402189 0.215400471
2496 0.0869714 ARMET PROTEIN PRECURSOR (ARGININE-RICH PROTEIN). [SWISSPROT;Acc:P55145] ARMET 0.403767 0.215399971
2497 0.158519 SH3-CONTAINING GRB2-LIKE PROTEIN 2 (SH3 DOMAIN PROTEIN 2A) (ENDOPHILIN 1) (EEN-B1). [SWISSPROT;Acc:Q99962] SH3GL2 0.735941 0.215396343
2498 0.167149 "UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX CORE PROTEIN I, MITOCHONDRIAL PRECURSOR (EC 1.10.2.2). [SWISSPROT;Acc:P31930]" UQCRC1 0.776201 0.215342418
2499 0.235517 "MITOCHONDRIAL PROCESSING PEPTIDASE ALPHA SUBUNIT, MITOCHONDRIAL PRECURSOR (EC 3.4.24.64) (ALPHA-MPP) (P-55) (HA1523). [SWISSPROT;Acc:Q10713]" PMPCA 1.09378 0.215323923
2500 0.208649 "MITOCHONDRIAL PROCESSING PEPTIDASE BETA SUBUNIT, MITOCHONDRIAL PRECURSOR (EC 3.4.24.64) (BETA-MPP) (P-52). [SWISSPROT;Acc:O75439]" PMPCB 0.969013 0.215321157
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 0.800978 0.215238121
2502 1.02862 KERATIN ASSOCIATED PROTEIN 9-4; KERATIN ASSOCIATED PROTEIN 9.4. [RefSeq;Acc:NM_033191] no value 4.7857 0.214936164
2503 0.26445 JUNCTIONAL ADHESION MOLECULE 1 PRECURSOR (JAM) (PLATELET ADHESION MOLECULE 1) (PAM-1) (PLATELET F11 RECEPTOR). [SWISSPROT;Acc:Q9Y624] F11R 1.23096 0.214832326
2504 0.174979 ORNITHINE DECARBOXYLASE ANTIZYME INHIBITOR. [SWISSPROT;Acc:O14977] AZIN1 0.814661 0.214787501
2505 0.177719 ORNITHINE DECARBOXYLASE-LIKE PROTEIN (EC 4.1.1.17) (ODC-PARALOGUE) (ODC-P). [SWISSPROT;Acc:Q96A70] ADC 0.827431 0.214784073
2506 0.0405241 "PLECKSTRIN HOMOLOGY DOMAIN CONTAINING, FAMILY C (WITH FERM DOMAIN) MEMBER 1; MITOGEN INDUCIBLE 2; KINDLIN 2. [RefSeq;Acc:NM_006832]" PLEKHC1 0.188688 0.214767765
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/