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 352 to 401 of 3206 in total 
Rank	description	measured	expected	final	Hugo	
352	ALPHA-ACTININ 4 (NON-MUSCLE ALPHA-ACTININ 4) (F-ACTIN CROSS LINKING PROTEIN). [Source:SWISSPROT;Acc:O43707]	1.5119	5.35346	0.282415485	ACTN4	
353	TRANSCRIPTION INITIATION FACTOR TFIID 55 KDA SUBUNIT (TAFII-55) (TAFII55). [Source:SWISSPROT;Acc:Q15545]	0.124527	0.441415	0.282108673	TAF7	
354	"TATA BOX BINDING PROTEIN-ASSOCIATED FACTOR, RNA POLYMERASE II, Q; TAF7-LIKE RNA POLYMERASE II, TATA BOX BINDING PROTEIN (TBP)-ASSOCIATED FACTOR, 50 KD; TBP-ASSOCIATED FACTOR, RNA POLYMERASE II, Q. [Source:RefSeq;Acc:NM_024885]"	0.103996	0.36903	0.281809067	TAF7L	
355	EXOCYST COMPLEX COMPONENT SEC15B. [Source:SWISSPROT;Acc:Q9Y2D4]	0.117602	0.417668	0.281568135	EXOC6B	
356		0.0483186	0.171674	0.281455549		
357		0.042516	0.151058	0.281454805		
358	PROTEIN AD-016 (PROTEIN CGI-116) (X0009). [Source:SWISSPROT;Acc:Q9Y3C0]	0.3145	1.11741	0.281454435	CCDC53	
359	"CLEAVAGE AND POLYADENYLATION SPECIFIC FACTOR 5, 25 KD SUBUNIT; PRE-MRNA CLEAVAGE FACTOR IM (25KD); PRE-MRNA CLEAVAGE FACTOR IM, 25KD SUBUNIT. [Source:RefSeq;Acc:NM_007006]"	0.288916	1.0267	0.281402552	NUDT21	
360	EXOCYST COMPLEX COMPONENT SEC15A. [Source:SWISSPROT;Acc:Q8TAG9]	0.138286	0.49236	0.280863596	EXOC6	
361	EXOCYST COMPLEX COMPONENT SEC8. [Source:SWISSPROT;Acc:Q96A65]	0.090885	0.324189	0.280345724	EXOC4	
362	OSTEOCLAST STIMULATING FACTOR 1. [Source:SWISSPROT;Acc:Q92882]	0.0741822	0.264688	0.2802628	OSTF1	
363	SPLICING FACTOR 3B SUBUNIT 4 (SPLICEOSOME ASSOCIATED PROTEIN 49) (SAP 49) (SF3B50) (PRE-MRNA SPLICING FACTOR SF3B 49 KDA SUBUNIT). [Source:SWISSPROT;Acc:Q15427]	0.0893365	0.318821	0.280208957	SF3B4	
364	"C316G12.2 (NOVEL PROTEIN SIMILAR TO PREDICTED YEAST, WORM AND ARCHAE- BACTERIAL PROTEINS) (SIMILAR TO UND313) (S. CERVISIAE) (HYPOTHETICAL PROTEIN). [Source:SPTREMBL;Acc:Q9UJK0]"	0.131623	0.469919	0.280097208	C16orf42	
365	G-RICH SEQUENCE FACTOR-1 (GRSF-1). [Source:SWISSPROT;Acc:Q12849]	0.170665	0.610067	0.279747962	GRSF1	
366	HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN H3 (HNRNP H3) (HNRNP 2H9). [Source:SWISSPROT;Acc:P31942]	0.179445	0.641462	0.279743773	HNRPH3	
367	HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN F (HNRNP F). [Source:SWISSPROT;Acc:P52597]	0.198738	0.710442	0.279738529	HNRPF	
368	HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN H (HNRNP H). [Source:SWISSPROT;Acc:P31943]	0.219762	0.785612	0.279733507	HNRPH1	
369	HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN H' (HNRNP H') (FTP-3). [Source:SWISSPROT;Acc:P55795]	0.222111	0.794014	0.279731844	HNRPH2	
370	"COFILIN, NON-MUSCLE ISOFORM (18 KDA PHOSPHOPROTEIN) (P18). [Source:SWISSPROT;Acc:P23528]"	0.0460179	0.164816	0.279207723	CFL1	
371	DESTRIN (ACTIN-DEPOLYMERIZING FACTOR) (ADF). [Source:SWISSPROT;Acc:P18282]	0.0460179	0.164816	0.279207723	DSTN	
372	"COFILIN, MUSCLE ISOFORM (COFILIN 2). [Source:SWISSPROT;Acc:Q9Y281]"	0.0460179	0.164816	0.279207723	CFL2	
373		0.034272	0.122748	0.279206179		
374	UBIQUITIN FUSION DEGRADATION PROTEIN 1 HOMOLOG (UB FUSION PROTEIN 1). [Source:SWISSPROT;Acc:Q92890]	0.379312	1.35854	0.279205618	UFD1L	
375	"DYNEIN INTERMEDIATE CHAIN 2, CYTOSOLIC (DH IC-2) (CYTOPLASMIC DYNEIN INTERMEDIATE CHAIN 2). [Source:SWISSPROT;Acc:Q13409]"	0.119541	0.428154	0.279200942	DYNC1I2	
376	PRE-MRNA SPLICING FACTOR PRP17 (HPRP17) (EH-BINDING PROTEIN 3) (EHB3). [Source:SWISSPROT;Acc:O60508]	0.274292	0.982579	0.279155162	CDC40	
377		0.0389719	0.139616	0.279136345	CCDC12	
378	PTB DOMAIN ADAPTOR PROTEIN CED-6; ENGULFMENT ADAPTER PROTEIN. [Source:RefSeq;Acc:NM_016315]	0.0573826	0.205572	0.279136264	GULP1	
379	CROOKED NECK-LIKE PROTEIN 1 (CROOKED NECK HOMOLOG) (HCRN) (CGI-201) (MSTP021). [Source:SWISSPROT;Acc:Q9BZJ0]	0.802935	2.8765	0.279136103	CRNKL1	
380	CALCYPHOSINE. [Source:SWISSPROT;Acc:Q13938]	0.0480742	0.172225	0.279136014	CAPS	
381		0.0666911	0.23892	0.279135694	CAPSL	
382	MITOCHONDRIAL IMPORT RECEPTOR SUBUNIT TOM20 HOMOLOG (MITOCHONDRIAL 20 KDA OUTER MEMBRANE PROTEIN) (OUTER MITOCHONDRIAL MEMBRANE RECEPTOR TOM20). [Source:SWISSPROT;Acc:Q15388]	0.0530069	0.189914	0.279110018	TOMM20	
383	PEROXISOMAL FARNESYLATED PROTEIN (33 KDA HOUSEKEEPING PROTEIN) (PEROXIN 19). [Source:SWISSPROT;Acc:P40855]	0.245859	0.88087	0.27910929	PEX19	
384	CDC42-INTERACTING PROTEIN 4 (THYROID RECEPTOR INTERACTING PROTEIN 10) (TRIP-10). [Source:SWISSPROT;Acc:Q15642]	0.448126	1.60594	0.279042804	TRIP10	
385	"DYNEIN INTERMEDIATE CHAIN 1, CYTOSOLIC (DH IC-1) (CYTOPLASMIC DYNEIN INTERMEDIATE CHAIN 1). [Source:SWISSPROT;Acc:O14576]"	0.104222	0.373698	0.278893652	DYNC1I1	
386	"GRPE PROTEIN HOMOLOG 2, MITOCHONDRIAL PRECURSOR (MT-GRPE#2). [Source:SWISSPROT;Acc:Q8TAA5]"	0.0678064	0.243254	0.278747318	GRPEL2	
387	"GRPE PROTEIN HOMOLOG 1, MITOCHONDRIAL PRECURSOR (MT-GRPE#1) (HMGE). [Source:SWISSPROT;Acc:Q9HAV7]"	0.0851715	0.305551	0.278747247	GRPEL1	
388	"SWI/SNF RELATED, MATRIX ASSOCIATED, ACTIN DEPENDENT REGULATOR OF CHROMATIN SUBFAMILY D MEMBER 1 (SWI/SNF COMPLEX 60 KDA SUBUNIT) (BRG1- ASSOCIATED FACTOR 60A). [Source:SWISSPROT;Acc:Q96GM5]"	0.140567	0.504282	0.278746812	SMARCD1	
389	SWI/SNF-RELATED MATRIX-ASSOCIATED ACTIN-DEPENDENT REGULATOR OF CHROMATIN D2; RSC6P; MAMMALIAN CHROMATIN REMODELING COMPLEX BRG1-ASSOCIATED FACTOR 60B; SWP73-LIKE PROTEIN; CHROMATIN REMODELING COMPLEX BAF60B SUBUNIT; SWI/SNF COMPLEX 60 KDA SUBUNIT B. [Sour	0.0474703	0.170299	0.278746792	SMARCD2	
390	SWI/SNF-RELATED MATRIX-ASSOCIATED ACTIN-DEPENDENT REGULATOR OF CHROMATIN D3; RSC6P; MAMMALIAN CHROMATIN REMODELING COMPLEX BRG1-ASSOCIATED FACTOR 60C; SWP73-LIKE PROTEIN; CHROMATIN REMODELING COMPLEX BAF60C SUBUNIT; SWI/SNF COMPLEX 60 KDA SUBUNIT C. [Sour	0.123465	0.44293	0.278746077	SMARCD3	
391		0.368426	1.32182	0.278726302	FNBP1L	
392	40S RIBOSOMAL PROTEIN S26. [Source:SWISSPROT;Acc:P02383]	0.135061	0.484774	0.278606113		
393	MITOCHONDRIAL IMPORT INNER MEMBRANE TRANSLOCASE SUBUNIT TIM22. [Source:SWISSPROT;Acc:Q9Y584]	0.0993399	0.356562	0.278604843	TIMM22	
394	ATP SYNTHASE MITOCHONDRIAL F1 COMPLEX ASSEMBLY FACTOR 2. [Source:RefSeq;Acc:NM_145691]	0.0993399	0.356562	0.278604843	ATPAF2	
395	UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 14 KDA PROTEIN (EC 1.10.2.2) (COMPLEX III SUBUNIT VI) (QP-C). [Source:SWISSPROT;Acc:P14927]	0.0993399	0.356562	0.278604843	UQCRB	
396		0.0370257	0.132897	0.278604483	TSR2	
397	NHP2-LIKE PROTEIN 1 (HIGH MOBILITY GROUP-LIKE NUCLEAR PROTEIN 2 HOMOLOG 1) ([U4/U6.U5] TRI-SNRNP 15.5 KDA PROTEIN) (OTK27). [Source:SWISSPROT;Acc:P55769]	0.0337208	0.121119	0.278410489	NHP2L1	
398	NUCLEAR FRAGILE X MENTAL RETARDATION PROTEIN INTERACTING PROTEIN 1; NUCLEAR FRAGILE X MENTAL RETARDATION INTERCATING PROTEIN 1; NUCLEAR FRAGILE X MENTAL RETARDATION PROTEIN-INTERACTING PROTEIN 1. [Source:RefSeq;Acc:NM_012345]	0.0673151	0.241784	0.278410068	NUFIP1	
399	THYROID RECEPTOR INTERACTING PROTEIN 3 (TRIP-3) (FRAGMENT). [Source:SWISSPROT;Acc:Q15649]	0.0671887	0.24133	0.278410061	ZNHIT3	
400	TRANSCRIPTION INITIATION FACTOR IIB (GENERAL TRANSCRIPTION FACTOR TFIIB) (S300-II). [Source:SWISSPROT;Acc:Q00403]	0.101036	0.362904	0.278409717	GTF2B	
401	M-PHASE INDUCER PHOSPHATASE 3 (EC 3.1.3.48) (DUAL SPECIFICITY PHOSPHATASE CDC25C). [Source:SWISSPROT;Acc:P30307]	0.590395	2.12136	0.278309669	CDC25C	

Legend:
- Rank is the rank after comparing the two networks
- Hugo is the bloody hugo identifier as demanded by the BMC Bioinformatics idiots
- http://analysis.yellowcouch.org/