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.


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Rank Gene measured expected description Hugo final
Results: HTML CSV LaTeX Showing element 551 to 600 of 3206 in total
Rank
measured
expected
description
Hugo
final
551 0.046789 0.172653 TBC1 DOMAIN FAMILY PROTEIN C22ORF4. [SWISSPROT;Acc:Q8WUA7] TBC1D22A 0.271000214
552 NUCLEAR RECEPTOR COACTIVATOR 7; ESTROGEN RECEPTOR ASSOCIATED PROTEIN 140 KDA. [RefSeq;Acc:NM_181782] NCOA7
553 0.0385424 0.142223 "LATS, LARGE TUMOR SUPPRESSOR, HOMOLOG 2; LATS (LARGE TUMOR SUPPRESSOR, DROSOPHILA) HOMOLOG 2. [RefSeq;Acc:NM_014572]" LATS2 0.270999768
554 0.0368814 0.136094 SH3 DOMAIN-BINDING GLUTAMIC ACID-RICH-LIKE PROTEIN 2 (FOVEA-ASSOCIATED SH3 DOMAIN BINDING PROTEIN). [SWISSPROT;Acc:Q9UJC5] no value 0.270999456
555 0.0362497 0.133763 DJ132F21.2 (CONTAINS A NOVEL PROTEIN SIMILAR TO THE L82E FROM DROSOPHILA) (FRAGMENT). [SPTREMBL;Acc:Q9H125] C20orf118 0.270999454
556 0.0371738 0.137173 SH3 DOMAIN-BINDING GLUTAMIC ACID-RICH-LIKE PROTEIN. [SWISSPROT;Acc:O75368] SH3BGRL 0.270999395
557 0.0380979 0.140583 OXIDATION RESISTANCE 1. [RefSeq;Acc:NM_181354] OXR1 0.270999338
558 0.50366 1.85853 DYMECLIN. [RefSeq;Acc:NM_017653] DYM 0.270999123
559 0.0359807 0.132771 TBC1 DOMAIN FAMILY PROTEIN C22ORF4-LIKE (FRAGMENT). [SWISSPROT;Acc:Q9NU19] TBC1D22B 0.270998185
560 0.539175 1.99055 ELAV-LIKE PROTEIN 3 (HU-ANTIGEN C) (HUC) (PARANEOPLASTIC CEREBELLAR DEGENERATION-ASSOCIATED ANTIGEN) (PARANEOPLASTIC LIMBIC ENCEPHALITIS ANTIGEN 21). [SWISSPROT;Acc:Q14576] no value 0.270867348
561 0.0483159 0.178411 POLYPEPTIDE N-ACETYLGALACTOSAMINYLTRANSFERASE 2; UDP-GALNAC TRANSFERASE 2. [RefSeq;Acc:NM_004481] GALNT2 0.270812338
562 1.06428 3.92996 RAD54L2 0.270811917
563 0.230346 0.850576 BTBD9 0.270811779
564 0.0370824 0.136931 SIMILAR TO EXPRESSED SEQUENCE AI415388 (FRAGMENT). [SPTREMBL;Acc:Q8N428] GALNTL1 0.270810846
565 0.1722 0.635895 "SERINE/THREONINE PROTEIN PHOSPHATASE 2A, 65 KDA REGULATORY SUBUNIT A, ALPHA ISOFORM (PP2A, SUBUNIT A, PR65-ALPHA ISOFORM) (PP2A, SUBUNIT A, R1-ALPHA ISOFORM) (MEDIUM TUMOR ANTIGEN-ASSOCIATED 61 KDA PROTEIN). [SWISSPROT;Acc:P30153]" PPP2R1A 0.270799424
566 0.449826 1.66144 ELAV-LIKE PROTEIN 1 (HU-ANTIGEN R) (HUR). [SWISSPROT;Acc:Q15717] ELAVL1 0.270744655
567 0.136702 0.504965 DHRS7B 0.270715792
568 0.0932883 0.344638 SIMILAR TO KINASE SUPPRESSOR OF RAS (FRAGMENT). [SPTREMBL;Acc:Q8IVT5] KSR1 0.270684893
569 0.251342 0.928542 DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 2 (EC 2.7.1.-) (MAP KINASE KINASE 2) (MAPKK 2) (ERK ACTIVATOR KINASE 2) (MAPK/ERK KINASE 2) (MEK2). [SWISSPROT;Acc:P36507] MAP2K2 0.270684579
570 DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 1 (EC 2.7.1.-) (MAP KINASE KINASE 1) (MAPKK 1) (ERK ACTIVATOR KINASE 1) (MAPK/ERK KINASE 1) (MEK1). [SWISSPROT;Acc:Q02750] MAP2K1
571 0.0726249 0.268301 KSR2 0.270684418
572 0.495507 1.83073 ELAV-LIKE PROTEIN 4 (PARANEOPLASTIC ENCEPHALOMYELITIS ANTIGEN HUD) (HU-ANTIGEN D). [SWISSPROT;Acc:P26378] ELAVL4 0.270660884
573 0.181797 0.671805 "SERINE/THREONINE PROTEIN PHOSPHATASE 2A, 65 KDA REGULATORY SUBUNIT A, BETA ISOFORM (PP2A, SUBUNIT A, PR65-BETA ISOFORM) (PP2A, SUBUNIT A, R1-BETA ISOFORM). [SWISSPROT;Acc:P30154]" PPP2R1B 0.270609775
574 0.495602 1.83168 ELAV-LIKE PROTEIN 2 (HU-ANTIGEN B) (HUB) (ELAV-LIKE NEURONAL PROTEIN 1) (NERVOUS SYSTEM-SPECIFIC RNA BINDING PROTEIN HEL-N1). [SWISSPROT;Acc:Q12926] ELAVL2 0.270572371
575 0.200205 0.740509 BILE ACID COENZYME A: AMINO ACID N-ACYLTRANSFERASE; GLYCINE N-CHOLOYLTRANSFERASE. [RefSeq;Acc:NM_001701] BAAT 0.270361333
576 0.230682 0.853273 PEROXISOMAL ACYL-COENZYME A THIOESTER HYDROLASE 2A (EC 3.1.2.2) (PEROXISOMAL LONG-CHAIN ACYL-COA THIOESTERASE 2) (ZAP128). [SWISSPROT;Acc:P49753] ACOT1 0.270349583
577 0.257341 0.951909 PEROXISOMAL ACYL-COA THIOESTERASE 2B; LIKELY ORTHOLOG OF MOUSE PEROXISOMAL ACYL-COA THIOESTERASE 2B. [RefSeq;Acc:NM_152331] ACOT4 0.270342018
578 0.565201 2.09213 IRF2BP2 0.270155774
579 0.483254 1.78896 C14orf4 0.270131249
580 0.404388 1.49712 HEPATOCYTE NUCLEAR FACTOR 3-ALPHA (HNF-3A) (FORKHEAD BOX PROTEIN A1). [SWISSPROT;Acc:P55317] FOXA1 0.270110612
581 0.334862 1.23982 UBIQUITIN-LIKE PROTEIN SUMO-1 CONJUGATING ENZYME (EC 6.3.2.19) (SUMO- 1-PROTEIN LIGASE) (UBIQUITIN CARRIER PROTEIN) (UBIQUITIN-CONJUGATING ENZYME UBCE2A) (P18). [SWISSPROT;Acc:P50550] UBE2I 0.270089206
582 0.0948257 0.351165 "SERINE/THREONINE PROTEIN PHOSPHATASE 2A, 55 KDA REGULATORY SUBUNIT B, ALPHA ISOFORM (PP2A, SUBUNIT B, B-ALPHA ISOFORM) (PP2A, SUBUNIT B, B55-ALPHA ISOFORM) (PP2A, SUBUNIT B, PR55-ALPHA ISOFORM) (PP2A, SUBUNIT B, R2-ALPHA ISOFORM). [SWISSPROT;Acc:Q0" no value 0.270031751
583 0.0951162 0.352242 UNCHARACTERIZED HEMATOPOIETIC STEM/PROGENITOR CELLS PROTEIN MDS026. [SPTREMBL;Acc:Q9NZ48] PPP2R2D 0.270030831
584 0.0961987 0.356254 "SERINE/THREONINE PROTEIN PHOSPHATASE 2A, 55 KDA REGULATORY SUBUNIT B, BETA ISOFORM (PP2A, SUBUNIT B, B-BETA ISOFORM) (PP2A, SUBUNIT B, B55- BETA ISOFORM) (PP2A, SUBUNIT B, PR55-BETA ISOFORM) (PP2A, SUBUNIT B, R2-BETA ISOFORM). [SWISSPROT;Acc:Q00005" PPP2R2B 0.270028407
585 0.101295 0.375141 "SERINE/THREONINE PROTEIN PHOSPHATASE 2A, 55 KDA REGULATORY SUBUNIT B, GAMMA ISOFORM (PP2A, SUBUNIT B, B-GAMMA ISOFORM) (PP2A, SUBUNIT B, B55-GAMMA ISOFORM) (PP2A, SUBUNIT B, PR55-GAMMA ISOFORM) (PP2A, SUBUNIT B, R2-GAMMA ISOFORM) (IMYPNO1). [SWISSP" PPP2R2C 0.270018473
586 0.673422 2.49889 CYCLIC-AMP-DEPENDENT TRANSCRIPTION FACTOR ATF-2 (ACTIVATING TRANSCRIPTION FACTOR 2) (CAMP RESPONSE ELEMENT BINDING PROTEIN CRE- BP1) (HB16). [SWISSPROT;Acc:P15336] ATF2 0.269488453
587 0.574984 2.13394 CYCLIC-AMP-DEPENDENT TRANSCRIPTION FACTOR ATF-7 (ACTIVATING TRANSCRIPTION FACTOR 7) (TRANSCRIPTION FACTOR ATF-A). [SWISSPROT;Acc:P17544] ATF7 0.269447126
588 0.122515 0.454799 40S RIBOSOMAL PROTEIN S8. [SWISSPROT;Acc:P09058] RPS8 0.269382738
589 0.393043 1.45917 PGM2L1 0.269360664
590 0.12174 0.452001 5'-METHYLTHIOADENOSINE PHOSPHORYLASE (EC 2.4.2.28) (MTA PHOSPHORYLASE) (MTAPASE). [SWISSPROT;Acc:Q13126] MTAP 0.269335687
591 PUTATIVE RIBOSOMAL RNA METHYLTRANSFERASE 1 (EC 2.1.1.-) (RRNA (URIDINE-2'-O-)-METHYLTRANSFERASE) (JM23 PROTEIN). [SWISSPROT;Acc:Q9UET6] FTSJ1
592 0.0341846 0.126926 "SPECTRIN BETA CHAIN, BRAIN 2 (SPECTRIN, NON-ERYTHROID BETA CHAIN 2) (BETA-III SPECTRIN). [SWISSPROT;Acc:O15020]" SPTBN2 0.269327009
593 0.460943 1.71147 PGM2 0.269325784
594 0.537765 1.99671 PHOSPHOACETYLGLUCOSAMINE MUTASE (EC 5.4.2.3) (PAGM) (ACETYLGLUCOSAMINE PHOSPHOMUTASE) (N-ACETYLGLUCOSAMINE-PHOSPHATE MUTASE) (PHOSPHOGLUCOMUTASE 3). [SWISSPROT;Acc:O95394] PGM3 0.269325541
595 0.0426374 0.158312 "SPECTRIN BETA CHAIN, BRAIN 1 (SPECTRIN, NON-ERYTHROID BETA CHAIN 1) (BETA-II SPECTRIN) (FODRIN BETA CHAIN). [SWISSPROT;Acc:Q01082]" SPTBN1 0.26932513
596 0.414022 1.53743 HEPATOCYTE NUCLEAR FACTOR 3-BETA (HNF-3B) (FORKHEAD BOX PROTEIN A2). [SWISSPROT;Acc:Q9Y261] FOXA2 0.269294862
597 0.126132 0.468539 LIM DOMAIN ONLY 7; ZINC-FINGER DOMAIN-CONTAINING PROTEIN; LOMP PROTEIN; F-BOX ONLY PROTEIN 20; F-BOX PROTEIN FBX20. [RefSeq;Acc:NM_005358] LMO7 0.269202777
598 0.132014 0.490424 CAMP RESPONSE ELEMENT-BINDING PROTEIN CRE-BPA. [RefSeq;Acc:NM_004904] CREB5 0.2691834
599 0.307359 1.14212 ZINC FINGER PROTEIN ZIC 2 (ZINC FINGER PROTEIN OF THE CEREBELLUM 2). [SWISSPROT;Acc:O95409] ZIC2 0.269112703
600 0.25098 0.932647 ZINC FINGER PROTEIN ZIC 3 (ZINC FINGER PROTEIN OF THE CEREBELLUM 3). [SWISSPROT;Acc:O60481] ZIC3 0.269105031

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/