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 Hugo expected final
Results: HTML CSV LaTeX Showing element 2458 to 2507 of 3206 in total
Rank
description
measured
Hugo
expected
final
2458 0.565608 OXSM 2.60988 0.21671801
2459 0.027214 C20orf80 0.125575 0.21671511
2460 BROMODOMAIN CONTAINING 7; BROMODOMAIN PROTEIN; BROMODOMAIN-CONTAINING 7. [RefSeq;Acc:NM_013263] 0.26631 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 TRANSCRIPTIONAL ADAPTER 2-LIKE (ADA2-LIKE PROTEIN) (KL04P). [SWISSPROT;Acc:O75478] 0.42132 TADA2L 1.94413 0.216713903
2465 0.210228 BRD9 0.970087 0.21671046
2466 GALECTIN-4 (LACTOSE-BINDING LECTIN 4) (L-36 LACTOSE BINDING PROTEIN) (L36LBP) (ANTIGEN NY-CO-27). [SWISSPROT;Acc:P56470] 0.384329 LGALS4 1.77366 0.216686964
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 RNASEH2A 1.48248 0.21659449
2468 45 KDA CALCIUM-BINDING PROTEIN PRECURSOR (CAB45) (STROMAL CELL-DERIVED FACTOR 4) (SDF-4). [SWISSPROT;Acc:Q9BRK5] 0.0737619 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 BAND 4.1-LIKE PROTEIN 3 (4.1B) (DIFFERENTIALLY EXPRESSED IN ADENOCARCINOMA OF THE LUNG PROTEIN 1) (DAL-1). [SWISSPROT;Acc:Q9Y2J2] 0.115589 EPB41L3 0.533671 0.216592245
2472 0.139984 CUEDC2 0.646308 0.216590233
2473 PROTEIN 4.1 (BAND 4.1) (P4.1) (EPB4.1) (4.1R). [SWISSPROT;Acc:P11171] 0.0900531 EPB41 0.415778 0.216589382
2474 BAND 4.1-LIKE PROTEIN 2 (GENERALLY EXPRESSED PROTEIN 4.1) (4.1G). [SWISSPROT;Acc:O43491] 0.0915902 EPB41L2 0.422875 0.216589299
2475 BAND 4.1-LIKE PROTEIN 1 (NEURONAL PROTEIN 4.1) (4.1N). [SWISSPROT;Acc:Q9H4G0] 0.0882127 EPB41L1 0.407281 0.216589284
2476 0.0586202 LSM14A 0.270652 0.21658883
2477 SIMILAR TO TRNA SYNTHETASE CLASS II. [RefSeq;Acc:NM_152268] 0.205001 PARS2 0.946559 0.216574984
2478 GALECTIN-9 (HOM-HD-21) (ECALECTIN). [SWISSPROT;Acc:O00182] 0.522708 LGALS9 2.41413 0.216520237
2479 PRE-MRNA CLEAVAGE COMPLEX II PROTEIN PCF11 (FRAGMENT). [SWISSPROT;Acc:O94913] 0.251152 PCF11 1.15996 0.216517811
2480 CHROMODOMAIN Y-LIKE PROTEIN 2. [RefSeq;Acc:NM_152342] 0.549251 CDYL2 2.53881 0.216341908
2481 TESTIS-SPECIFIC CHROMODOMAIN PROTEIN Y PROTEIN 2. [SWISSPROT;Acc:Q9Y6F7] 0.659303 CDY2B 3.04797 0.216308888
2482 TESTIS-SPECIFIC CHROMODOMAIN Y PROTEIN 1. [SWISSPROT;Acc:Q9Y6F8] 0.663776 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 HEMK PROTEIN HOMOLOG (EC 2.1.1.-) (M.HSAHEMKP). [SWISSPROT;Acc:Q9Y5R4] 0.343973 HEMK1 1.59051 0.216265852
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 GPI 0.618915 0.216249404
2486 CEREBRAL CELL ADHESION MOLECULE. [RefSeq;Acc:NM_016174] 0.155588 CEECAM1 0.719698 0.216185122
2487 0.166202 GLT25D1 0.768906 0.21615386
2488 FIBULIN-2 PRECURSOR. [SWISSPROT;Acc:P98095] 0.195152 FBLN2 0.90295 0.216127139
2489 0.194172 no value 0.898593 0.216084479
2490 XPMC2 PREVENTS MITOTIC CATASTROPHE 2 HOMOLOG; XENOPUS PREVENTS MITOTIC CATASTROPHE 2 HOMOLOG. [RefSeq;Acc:NM_020385] 0.172887 REXO4 0.801332 0.215749527
2491 DEHYDRODOLICHYL DIPHOSPHATE SYNTHASE. [RefSeq;Acc:NM_024887] 0.238591 DHDDS 1.10654 0.215618956
2492 0.239571 no value 1.11109 0.215617997
2493 SH3-CONTAINING GRB2-LIKE PROTEIN 3 (SH3 DOMAIN PROTEIN 2C) (EEN-B2). [SWISSPROT;Acc:Q99963] 0.171407 SH3GL3 0.795244 0.215540136
2494 METHIONYL-TRNA SYNTHETASE (EC 6.1.1.10) (METHIONINE--TRNA LIGASE) (METRS). [SWISSPROT;Acc:P56192] 0.0641898 MARS 0.297931 0.2154519
2495 HISTIDINE DECARBOXYLASE (EC 4.1.1.22) (HDC). [SWISSPROT;Acc:P19113] 0.0866317 HDC 0.402189 0.215400471
2496 ARMET PROTEIN PRECURSOR (ARGININE-RICH PROTEIN). [SWISSPROT;Acc:P55145] 0.0869714 ARMET 0.403767 0.215399971
2497 SH3-CONTAINING GRB2-LIKE PROTEIN 2 (SH3 DOMAIN PROTEIN 2A) (ENDOPHILIN 1) (EEN-B1). [SWISSPROT;Acc:Q99962] 0.158519 SH3GL2 0.735941 0.215396343
2498 "UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX CORE PROTEIN I, MITOCHONDRIAL PRECURSOR (EC 1.10.2.2). [SWISSPROT;Acc:P31930]" 0.167149 UQCRC1 0.776201 0.215342418
2499 "MITOCHONDRIAL PROCESSING PEPTIDASE ALPHA SUBUNIT, MITOCHONDRIAL PRECURSOR (EC 3.4.24.64) (ALPHA-MPP) (P-55) (HA1523). [SWISSPROT;Acc:Q10713]" 0.235517 PMPCA 1.09378 0.215323923
2500 "MITOCHONDRIAL PROCESSING PEPTIDASE BETA SUBUNIT, MITOCHONDRIAL PRECURSOR (EC 3.4.24.64) (BETA-MPP) (P-52). [SWISSPROT;Acc:O75439]" 0.208649 PMPCB 0.969013 0.215321157
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] 0.172401 SH3GL1 0.800978 0.215238121
2502 KERATIN ASSOCIATED PROTEIN 9-4; KERATIN ASSOCIATED PROTEIN 9.4. [RefSeq;Acc:NM_033191] 1.02862 no value 4.7857 0.214936164
2503 JUNCTIONAL ADHESION MOLECULE 1 PRECURSOR (JAM) (PLATELET ADHESION MOLECULE 1) (PAM-1) (PLATELET F11 RECEPTOR). [SWISSPROT;Acc:Q9Y624] 0.26445 F11R 1.23096 0.214832326
2504 ORNITHINE DECARBOXYLASE ANTIZYME INHIBITOR. [SWISSPROT;Acc:O14977] 0.174979 AZIN1 0.814661 0.214787501
2505 ORNITHINE DECARBOXYLASE-LIKE PROTEIN (EC 4.1.1.17) (ODC-PARALOGUE) (ODC-P). [SWISSPROT;Acc:Q96A70] 0.177719 ADC 0.827431 0.214784073
2506 "PLECKSTRIN HOMOLOGY DOMAIN CONTAINING, FAMILY C (WITH FERM DOMAIN) MEMBER 1; MITOGEN INDUCIBLE 2; KINDLIN 2. [RefSeq;Acc:NM_006832]" 0.0405241 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/