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 description measured expected final Hugo
Results: HTML CSV LaTeX Showing element 408 to 457 of 3206 in total
Rank
description
measured
expected
final
Hugo
408 PUTATIVE PRE-MRNA SPLICING FACTOR RNA HELICASE (DEAH BOX PROTEIN 15) (ATP-DEPENDENT RNA HELICASE #46). [SWISSPROT;Acc:O43143] 0.603245 2.16897 0.278125101 DHX15
409 "BA138E2.1.2 (FORMIN-BINDING PROTEIN 17 (FBP17), ISOFORM 2). [SPTREMBL;Acc:Q96LH6]" 0.404169 1.45394 0.277981897 FNBP1
410 EYES ABSENT HOMOLOG 3. [SWISSPROT;Acc:Q99504] 2.06651 7.43888 0.27779854 EYA3
411 0.356784 1.28488 0.277678849 no value
412 ARGININE/SERINE-RICH SPLICING FACTOR 10 (TRANSFORMER-2-BETA) (HTRA2- BETA) (TRANSFORMER 2 PROTEIN HOMOLOG) (SILICA-INDUCED PROTEIN 41) (RA301). [SWISSPROT;Acc:Q15815] 0.368948 1.32916 0.277579825 SFRS10
413 0.197804 0.712745 0.27752422 CCDC49
414 SAL-LIKE PROTEIN 2 (ZINC FINGER PROTEIN SALL2) (HSAL2). [SWISSPROT;Acc:Q9Y467] 0.13272 0.478487 0.277374307 SALL2
415 SAL-LIKE PROTEIN 4 (ZINC FINGER PROTEIN SALL4). [SWISSPROT;Acc:Q9UJQ4] 0.135171 0.487324 0.277373985 SALL4
416 CLATHRIN COAT ASSEMBLY PROTEIN AP180 (CLATHRIN COAT ASSOCIATED PROTEIN AP180) (91 KDA SYNAPTOSOMAL-ASSOCIATED PROTEIN). [SWISSPROT;Acc:O60641] 0.212723 0.766919 0.277373491 SNAP91
417 ATROPHIN-1 (DENTATORUBRAL-PALLIDOLUYSIAN ATROPHY PROTEIN). [SWISSPROT;Acc:P54259] 0.13427 0.484077 0.277373228 ATN1
418 0.0384193 0.138512 0.277371636 C8orf79
419 SAL-LIKE PROTEIN 3 (ZINC FINGER PROTEIN SALL3) (HSALL3). [SWISSPROT;Acc:Q9BXA9] 0.148125 0.534032 0.277371019 SALL3
420 POLYPYRIMIDINE TRACT BINDING PROTEIN 2; NEURAL POLYPYRIMIDINE TRACT BINDING PROTEIN; PTB-LIKE PROTEIN. [RefSeq;Acc:NM_021190] 0.152427 0.549542 0.277370974 PTBP2
421 UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 8 (EC 3.1.2.15) (UBIQUITIN THIOLESTERASE 8) (UBIQUITIN-SPECIFIC PROCESSING PROTEASE 8) (DEUBIQUITINATING ENZYME 8). [SWISSPROT;Acc:P40818] 0.0884444 0.318867 0.277370816 USP8
422 ROD1 REGULATOR OF DIFFERENTIATION 1; FISSION YEAST DIFFERENTIATION REGULATOR; REGULATOR OF DIFFERENTIATION (IN S. POMBI) 1; REGULATOR OF DIFFERENTIATION (IN S. POMBE) 1. [RefSeq;Acc:NM_005156] 0.153277 0.552607 0.277370717 ROD1
423 ADAPTOR-ASSOCIATED KINASE 1. [RefSeq;Acc:NM_014911] 0.168547 0.60766 0.277370569 AAK1
424 0.0397949 0.143472 0.277370497 ARHGAP23
425 DEAD (ASP-GLU-ALA-ASP) BOX POLYPEPTIDE 47; HQP0256 PROTEIN. [RefSeq;Acc:NM_016355] 0.0884193 0.318777 0.277370387 no value
426 RHO-GTPASE ACTIVATING PROTEIN 10. [RefSeq;Acc:NM_020824] 0.0500251 0.180355 0.277370187 ARHGAP21
427 GROWTH-ARREST-SPECIFIC PROTEIN 7 (GAS-7). [SWISSPROT;Acc:O60861] 0.139845 0.504182 0.277370077 GAS7
428 PHOSPHATIDYLINOSITOL-BINDING CLATHRIN ASSEMBLY PROTEIN (CLATHRIN ASSEMBLY LYMPHOID MYELOID LEUKEMIA PROTEIN). [SWISSPROT;Acc:Q13492] 0.276961 0.998529 0.27736901 PICALM
429 SAL-LIKE PROTEIN 1 (ZINC FINGER PROTEIN SALL1) (SPALT-LIKE TRANSCRIPTION FACTOR 1) (HSAL1). [SWISSPROT;Acc:Q9NSC2] 0.176985 0.63809 0.277366829 SALL1
430 "CCR4-NOT TRANSCRIPTION COMPLEX, SUBUNIT 4; NOT4 (NEGATIVE REGULATOR OF TRANSCRIPTION 4, YEAST) HOMOLOG; CCR4-NOT TRANSCRIPTION COMPLEX, SUBUNIT. [RefSeq;Acc:NM_013316]" CNOT4
431 ARGININE-GLUTAMIC ACID DIPEPTIDE (RE) REPEATS; ATROPHIN 1-LIKE; ARGININE GLUTAMIC ACID DIPEPTIDE RE REPEATS. [RefSeq;Acc:NM_012102] RERE
432 "2-OXOISOVALERATE DEHYDROGENASE BETA SUBUNIT, MITOCHONDRIAL PRECURSOR (EC 1.2.4.4) (BRANCHED-CHAIN ALPHA-KETO ACID DEHYDROGENASE E1 COMPONENT BETA CHAIN) (BCKDH E1-BETA). [SWISSPROT;Acc:P21953]" BCKDHB
433 POLYPYRIMIDINE TRACT-BINDING PROTEIN 1 (PTB) (HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN I) (HNRNP I) (57 KDA RNA-BINDING PROTEIN PPTB-1). [SWISSPROT;Acc:P26599] PTBP1
434 MEMBRANE-ASSOCIATED NUCLEIC ACID BINDING PROTEIN. [RefSeq;Acc:NM_018835] RC3H2
435 EYES ABSENT HOMOLOG 4. [SWISSPROT;Acc:O95677] 1.76157 6.35359 0.277255851 EYA4
436 EYES ABSENT HOMOLOG 1. [SWISSPROT;Acc:Q99502] 1.76022 6.35074 0.2771677 EYA1
437 EYES ABSENT HOMOLOG 2. [SWISSPROT;Acc:O00167] 1.69676 6.12181 0.277166394 EYA2
438 TRANSFORMER-2 PROTEIN HOMOLOG (TRA-2 ALPHA). [SWISSPROT;Acc:Q13595] 0.345566 1.24774 0.276953532 no value
439 AF-6 PROTEIN. [SWISSPROT;Acc:P55196] 0.263953 0.953667 0.276776904 MLLT4
440 GLUTATHIONE S-TRANSFERASE THETA 2 (EC 2.5.1.18) (GST CLASS-THETA). [SWISSPROT;Acc:P30712] 0.182551 0.659693 0.276721142 GSTT2B
441 "ATPASE INHIBITOR, MITOCHONDRIAL PRECURSOR. [SWISSPROT;Acc:Q9UII2]" 0.0602832 0.217862 0.276703601 ATPIF1
442 POLYAMINE OXIDASE ISOFORM 1; POLYAMINE OXIDASE; FLAVIN-CONTAINING SPERMINE OXIDASE; PUTATIVE CYCLIN G1 INTERACTING PROTEIN; FLAVIN CONTAINING AMINE OXIDASE. [RefSeq;Acc:NM_019025] SMOX
443 PEROXISOMAL N1-ACETYL-SPERMINE/SPERMIDINE OXIDASE. [RefSeq;Acc:NM_152911] 0.0442587 0.15995 0.276703345 PAOX
444 CYTOCHROME C-TYPE HEME LYASE (EC 4.4.1.17) (CCHL) (HOLOCYTOCHROME C- TYPE SYNTHASE). [SWISSPROT;Acc:P53701] 0.0485005 0.17528 0.27670299 HCCS
445 GLUTATHIONE S-TRANSFERASE THETA 1 (EC 2.5.1.18) (GST CLASS-THETA) (GLUTATHIONE TRANSFERASE T1-1). [SWISSPROT;Acc:P30711] 0.230886 0.83446 0.276689116 GSTT1
446 0.260039 0.939933 0.276656953 NPLOC4
447 REGUCALCIN GENE PROMOTOR REGION RELATED PROTEIN; RGPR-P117. [RefSeq;Acc:NM_033127] 0.109365 0.395349 0.276629004 SEC16B
448 0.141581 0.511852 0.276605347 SEC16A
449 0.0621484 0.224949 0.276277734 TSNARE1
450 0.0374708 0.135742 0.27604426 ISY1
451 XPA-BINDING PROTEIN 2 (HCNP PROTEIN) (PP3898). [SWISSPROT;Acc:Q9HCS7] 0.441621 1.59982 0.27604418 XAB2
452 "PROTEIN-TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 1 (EC 3.1.3.48) (PROTEIN-TYROSINE PHOSPHATASE 1B) (PTP-1B). [SWISSPROT;Acc:P18031]" 0.215243 0.779889 0.27599184 no value
453 "PROTEIN-TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 2 (EC 3.1.3.48) (T- CELL PROTEIN-TYROSINE PHOSPHATASE) (TCPTP). [SWISSPROT;Acc:P17706]" 0.173881 0.6302 0.275913996 PTPN2
454 TRANSDUCIN BETA-LIKE 2 PROTEIN (WS BETA-TRANSDUCIN REPEATS PROTEIN) (WS-BETATRP) (WILLIAMS-BEUREN SYNDROME CHROMOSOME REGION 13 PROTEIN). [SWISSPROT;Acc:Q9Y4P3] 0.132041 0.478695 0.275835344 TBL2
455 MITOCHONDRIAL GTP BINDING PROTEIN ISOFORM V. [RefSeq;Acc:NM_032620] 0.270501 0.981155 0.275696501 GTPBP3
456 0.0394844 0.143261 0.275611646 ZMAT2
457 SQUAMOUS CELL CARCINOMA ANTIGEN RECOGNIZED BY T CELLS 1; U4/U6.U5 TRI-SNRNP-ASSOCIATED 110 KDA PROTEIN; IGE AUTOANTIGEN; SART1(259) PROTEIN; SART1(800) PROTEIN. [RefSeq;Acc:NM_005146] 0.35534 1.28928 0.275611194 SART1

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/