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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Hugo Rank Gene description measured expected final

Results: HTML CSV LaTeX

Showing element 2002 to 2051 of 3206 in total

Hugo	Rank	description	measured	expected	final	
NLK	1701	NEMO-LIKE KINASE; LIKELY ORTHOLOG OF MOUSE NEMO LIKE KINASE. [Source:RefSeq;Acc:NM_016231]	0.210207	0.883788	0.237847764	
NME2	2010	NUCLEOSIDE DIPHOSPHATE KINASE A (EC 2.7.4.6) (NDK A) (NDP KINASE A) (TUMOR METASTATIC PROCESS-ASSOCIATED PROTEIN) (METASTASIS INHIBITION FACTOR NM23) (NM23-H1). [Source:SWISSPROT;Acc:P15531]	0.494361	2.14316	0.230669199	
NME2P1	2011	PUTATIVE NUCLEOSIDE DIPHOSPHATE KINASE (EC 2.7.4.6) (NDK) (NDP KINASE). [Source:SWISSPROT;Acc:O60361]	0.480816	2.08449	0.230663616	
NME3	2065	NUCLEOSIDE DIPHOSPHATE KINASE 3 (EC 2.7.4.6) (NDK 3) (NDP KINASE 3) (NM23-H3) (DR-NM23). [Source:SWISSPROT;Acc:Q13232]	0.366443	1.59695	0.229464291	
NMNAT3	1682	NICOTINAMIDE NUCLEOTIDE ADENYLYLTRANSFERASE 3; PYRIDINE NUCLEOTIDE ADENYLYLTRANSFERASE 3. [Source:RefSeq;Acc:NM_178177]	0.192536	0.808409	0.238166572	
NOB1	1532	NIN ONE BINDING PROTEIN; ADENOCARCINOMA ANTIGEN RECOGNIZED BY T LYMPHOCYTES 4. [Source:RefSeq;Acc:NM_014062]	0.0805704	0.332683	0.2421837	
NOC3L	1334	AD24 PROTEIN. [Source:RefSeq;Acc:NM_022451]	0.290237	1.18321	0.24529627	
NOC4L	1507		0.511781	2.10953	0.242604277	
NOL1	1565	PROLIFERATING-CELL NUCLEOLAR ANTIGEN P120 (PROLIFERATION-ASSOCIATED NUCLEOLAR PROTEIN P120). [Source:SWISSPROT;Acc:P46087]	0.714168	2.96197	0.241112503	
NOL10	1416		0.651969	2.67215	0.243986677	
NOL14	1483		0.54526	2.24437	0.242945682	
NOL5A	1523	NUCLEOLAR PROTEIN NOP56 (NUCLEOLAR PROTEIN 5A). [Source:SWISSPROT;Acc:O00567]	0.66215	2.73239	0.242333635	
NOL6	1267	NUCLEOLAR RNA-ASSOCIATED PROTEIN ALPHA ISOFORM. [Source:RefSeq;Acc:NM_022917]	0.966893	3.91912	0.246711762	
NOLA1	256	"NUCLEOLAR PROTEIN FAMILY A, MEMBER 1; GAR1 PROTEIN. [Source:RefSeq;Acc:NM_018983]"	0.11305	0.363171	0.311285868	
NOLA2	1714	"NUCLEOLAR PROTEIN FAMILY A, MEMBER 2; COMPONENT OF THE H/ACA SNORNP. [Source:RefSeq;Acc:NM_017838]"	0.0909039	0.382985	0.237356293	
NONO	1676	"54 KDA NUCLEAR RNA- AND DNA-BINDING PROTEIN (P54(NRB)) (P54NRB) (55 KDA NUCLEAR PROTEIN) (NMT55) (NON-POU DOMAIN-CONTAINING OCTAMER- BINDING PROTEIN) (DNA-BINDING P52/P100 COMPLEX, 52 KDA SUBUNIT). [Source:SWISSPROT;Acc:Q15233]"	0.201833	0.847008	0.238289367	
NOSTRIN	1730	NOSTRIN. [Source:RefSeq;Acc:NM_052946]	0.02137	0.0901539	0.237039108	
NOVA1	1208	RNA-BINDING PROTEIN NOVA-1 (NEURO-ONCOLOGICAL VENTRAL ANTIGEN 1) (ONCONEURAL VENTRAL ANTIGEN-1) (PARANEOPLASTIC RI ANTIGEN) (VENTRAL NEURON-SPECIFIC PROTEIN 1). [Source:SWISSPROT;Acc:P51513]	0.107742	0.434244	0.248113964	
NPC2	272	EPIDIDYMAL SECRETORY PROTEIN E1 PRECURSOR (NIEMANN-PICK DISEASE TYPE C2 PROTEIN) (EPI-1) (HE1) (EPIDIDYMAL SECRETORY PROTEIN 14.6) (ESP14.6). [Source:SWISSPROT;Acc:Q15668]	0.115432	0.377878	0.305474254	
NPEPPS	2270	PUROMYCIN-SENSITIVE AMINOPEPTIDASE (EC 3.4.11.-) (PSA). [Source:SWISSPROT;Acc:P55786]	0.0267797	0.120229	0.222739106	
NPLOC4	446		0.260039	0.939933	0.276656953	
NR1H2	1582	OXYSTEROLS RECEPTOR LXR-BETA (LIVER X RECEPTOR BETA) (NUCLEAR ORPHAN RECEPTOR LXR-BETA) (UBIQUITOUSLY-EXPRESSED NUCLEAR RECEPTOR) (NUCLEAR RECEPTOR NER). [Source:SWISSPROT;Acc:P55055]	0.0824164	0.34213	0.240892059	
NR1H3	1579	OXYSTEROLS RECEPTOR LXR-ALPHA (LIVER X RECEPTOR ALPHA) (NUCLEAR ORPHAN RECEPTOR LXR-ALPHA). [Source:SWISSPROT;Acc:Q13133]	0.110811	0.460002	0.240892431	
NR2C1	1006	ORPHAN NUCLEAR RECEPTOR TR2. [Source:SWISSPROT;Acc:P13056]	0.211877	0.831867	0.254700571	
NR2E1	1007	ORPHAN NUCLEAR RECEPTOR NR2E1 (NUCLEAR RECEPTOR TLX) (TAILLESS HOMOLOG) (TLL) (HTLL). [Source:SWISSPROT;Acc:Q9Y466]	0.280845	1.10266	0.254697731	
NR4A1	2777	ORPHAN NUCLEAR RECEPTOR HMR (EARLY RESPONSE PROTEIN NAK1) (TR3 ORPHAN RECEPTOR). [Source:SWISSPROT;Acc:P22736]	0.508993	2.52853	0.201299965	
NR4A2	2775	ORPHAN NUCLEAR RECEPTOR NURR1 (IMMEDIATE-EARLY RESPONSE PROTEIN NOT) (TRANSCRIPTIONALLY INDUCIBLE NUCLEAR RECEPTOR). [Source:SWISSPROT;Acc:P43354]	0.603026	2.99447	0.201379877	
NR4A3	2776	NUCLEAR HORMONE RECEPTOR NOR-1 (NEURON-DERIVED ORPHAN RECEPTOR 1) (MITOGEN INDUCED NUCLEAR ORPHAN RECEPTOR). [Source:SWISSPROT;Acc:Q92570]	0.515632	2.56143	0.201306302	
NR6A1	907	ORPHAN NUCLEAR RECEPTOR NR6A1 (GERM CELL NUCLEAR FACTOR) (GCNF) (RETINOID RECEPTOR-RELATED TESTIS SPECIFIC RECEPTOR) (RTR). [Source:SWISSPROT;Acc:Q15406]	0.196675	0.76137	0.258317244	
NRD1	726	NARDILYSIN PRECURSOR (EC 3.4.24.61) (N-ARGININE DIBASIC CONVERTASE) (NRD CONVERTASE) (NRD-C). [Source:SWISSPROT;Acc:O43847]	0.0787172	0.297409	0.26467659	
NSF	1708	VESICLE-FUSING ATPASE (EC 3.6.4.6) (VESICULAR-FUSION PROTEIN NSF) (N- ETHYLMALEIMIDE SENSITIVE FUSION PROTEIN) (NEM-SENSITIVE FUSION PROTEIN). [Source:SWISSPROT;Acc:P46459]	0.15883	0.66831	0.23765917	
NSFL1C	675	P47 PROTEIN ISOFORM A. [Source:RefSeq;Acc:NM_016143]	0.0978055	0.367477	0.266154072	
NSMCE4A	3139		1.64337	25.135	0.065381739	
NSUN2	2400		0.100955	0.460869	0.219053571	
NSUN5	2399	WILLIAMS BEUREN SYNDROME CRITICAL REGION 20A ISOFORM 2; NOL1/NOP2/SUN GENE FAMILY MEMBER; WILLIAMS-BEUREN SYNDROME CRITICAL REGION PROTEIN 20 COPY A; WILLIAMS BEUREN SYNDROME CHROMOSOME REGION 20. [Source:RefSeq;Acc:NM_018044]	0.100955	0.460869	0.219053571	
NSUN5B	2402	WILLIAMS BEUREN SYNDROME CHROMOSOME REGION 20C ISOFORM 1. [Source:RefSeq;Acc:NM_032158]	0.0859883	0.392545	0.219053357	
NUAK1	1004	PROBABLE SERINE/THREONINE-PROTEIN KINASE KIAA0537 (EC 2.7.1.-). [Source:SWISSPROT;Acc:O60285]	0.139695	0.54802	0.25490858	
NUAK2	998		0.115392	0.452671	0.254913613	
NUBP1	2942	NUCLEOTIDE-BINDING PROTEIN 1 (NBP 1). [Source:SWISSPROT;Acc:P53384]	0.0819552	0.528466	0.155081311	
NUBP2	2943	NUCLEOTIDE BINDING PROTEIN 2 (NBP 2). [Source:SWISSPROT;Acc:Q9Y5Y2]	0.0819552	0.528466	0.155081311	
NUCB1	2212	NUCLEOBINDIN 1 PRECURSOR (CALNUC). [Source:SWISSPROT;Acc:Q02818]	0.0240186	0.106724	0.225053409	
NUCB2	2210	NUCLEOBINDIN 2 PRECURSOR (DNA-BINDING PROTEIN NEFA). [Source:SWISSPROT;Acc:P80303]	0.0283406	0.125928	0.225053999	
NUDT12	1959	NUDIX (NUCLEOSIDE DIPHOSPHATE LINKED MOIETY X)-TYPE MOTIF 12. [Source:RefSeq;Acc:NM_031438]	0.0196941	0.085173	0.231224684	
NUDT21	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	
NUFIP1	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	
NUMB	2652	NUMB PROTEIN HOMOLOG (H-NUMB) (PROTEIN S171). [Source:SWISSPROT;Acc:P49757]	0.130073	0.619508	0.209961776	
NUMBL	2653	NUMB-LIKE PROTEIN (NUMB-R). [Source:SWISSPROT;Acc:Q9Y6R0]	0.122765	0.584702	0.209961656	
NUP43	1415	NUCLEOPORIN NUP43 (P42). [Source:SWISSPROT;Acc:Q8NFH3]	0.149203	0.611499	0.243995493	
NUP54	1480	NUCLEOPORIN 54KDA; NUCLEOPORIN P54. [Source:RefSeq;Acc:NM_017426]	0.114912	0.472937	0.24297528	
NUP88	310	NUCLEAR PORE COMPLEX PROTEIN NUP88 (NUCLEOPORIN NUP88) (88 KDA NUCLEAR PORE COMPLEX PROTEIN). [Source:SWISSPROT;Acc:Q99567]	0.251667	0.851392	0.295594744	

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/