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 501 to 550 of 3206 in total

Rank	description	measured	expected	final	Hugo	
501	SPECTRIN SH3 DOMAIN BINDING PROTEIN 1; EPS8 BINDING PROTEIN; INTERACTOR PROTEIN ABLBP4; ABL-INTERACTOR PROTEIN 1 LONG; NAP1 BINDING PROTEIN. [Source:RefSeq;Acc:NM_005470]	0.281309	1.0262	0.274126876	ABI1	
502		0.0401445	0.146476	0.274068789	CDV3	
503	EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT 7 (EIF-3 ZETA) (EIF3 P66) (EIF3D). [Source:SWISSPROT;Acc:O15371]	0.367035	1.33921	0.274068294	EIF3D	
504	ENIGMA PROTEIN; LIM DOMAIN PROTEIN. [Source:RefSeq;Acc:NM_005451]	0.0286746	0.104626	0.274067631		
505	INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE 1 (EC 1.1.1.205) (IMP DEHYDROGENASE 1) (IMPDH-I) (IMPD 1). [Source:SWISSPROT;Acc:P20839]	0.183159	0.66836	0.274042432	IMPDH1	
506	INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE 2 (EC 1.1.1.205) (IMP DEHYDROGENASE 2) (IMPDH-II) (IMPD 2). [Source:SWISSPROT;Acc:P12268]	0.157432	0.574482	0.274041658	IMPDH2	
507	GMP SYNTHASE [GLUTAMINE-HYDROLYZING] (EC 6.3.5.2) (GLUTAMINE AMIDOTRANSFERASE) (GMP SYNTHETASE). [Source:SWISSPROT;Acc:P49915]	0.348668	1.27232	0.274041122	GMPS	
508	HEAT SHOCK FACTOR BINDING PROTEIN 1. [Source:SWISSPROT;Acc:O75506]	0.135095	0.493083	0.273980243		
509	"RNA, U TRANSPORTER 1; SNURPORTIN-1. [Source:RefSeq;Acc:NM_005701]"	0.0968147	0.353554	0.273832852	SNUPN	
510		0.250323	0.914445	0.27374309	KIAA1217	
511	PROTEIN KINASE CLK2 (EC 2.7.1.-) (CDC-LIKE KINASE 2). [Source:SWISSPROT;Acc:P49760]	0.131932	0.482648	0.273350351	CLK2	
512	PROTEIN KINASE CLK3 (EC 2.7.1.-) (CDC-LIKE KINASE 3). [Source:SWISSPROT;Acc:P49761]	0.1005	0.367745	0.273287196	CLK3	
513	NUCLEAR PROTEIN SKIP (SKI-INTERACTING PROTEIN) (SNW1 PROTEIN) (NUCLEAR RECEPTOR COACTIVATOR NCOA-62). [Source:SWISSPROT;Acc:Q13573]	0.541777	1.98406	0.273064827	SNW1	
514	RNA-BINDING PROTEIN 9 (RNA BINDING MOTIF PROTEIN 9) (HEXARIBONUCLEOTIDE BINDING PROTEIN 2) (REPRESSOR OF TAMOXIFEN TRANSCRIPTIONAL ACTIVITY). [Source:SWISSPROT;Acc:O43251]	0.424547	1.55794	0.27250536	RBM9	
515	ATAXIN 2-BINDING PROTEIN. [Source:SWISSPROT;Acc:Q9NWB1]	0.534301	1.96129	0.272423252		
516		0.0480412	0.176368	0.272391817	METT10D	
517		0.313715	1.15171	0.272390619	UBAP2L	
518	M-PHASE INDUCER PHOSPHATASE 2 (EC 3.1.3.48) (DUAL SPECIFICITY PHOSPHATASE CDC25B). [Source:SWISSPROT;Acc:P30305]	0.510382	1.8743	0.272305394	CDC25B	
519	"BREAST CARCINOMA AMPLIFIED SEQUENCE 2; SPLICEOSOME ASSOCIATED PROTEIN, AMPLIFIED IN BREAST CANCER. [Source:RefSeq;Acc:NM_005872]"	0.0379775	0.139495	0.272249901	BCAS2	
520	"CDC5-LIKE; CDC5 (CELL DIVISION CYCLE 5, S. POMBE, HOMOLOG)-LIKE; CELL DIVISION CYCLE 5, S. POMBE, HOMOLOG-LIKE; CDC5-RELATED PROTEIN. [Source:RefSeq;Acc:NM_001253]"	0.333016	1.2232	0.272249836	CDC5L	
521	RNA-BINDING PROTEIN WITH MULTIPLE SPLICING (RBP-MS). [Source:SWISSPROT;Acc:Q93062]	0.504359	1.85404	0.272032426	RBPMS	
522	"PRE-MRNA CLEAVAGE FACTOR I, 59 KDA SUBUNIT. [Source:RefSeq;Acc:NM_024811]"	0.694134	2.5522	0.271974767		
523	"1,4-ALPHA-GLUCAN BRANCHING ENZYME (EC 2.4.1.18) (GLYCOGEN BRANCHING ENZYME) (BRANCHER ENZYME). [Source:SWISSPROT;Acc:Q04446]"	0.142881	0.525483	0.271904134	GBE1	
524	"GLYCOGEN PHOSPHORYLASE, MUSCLE FORM (EC 2.4.1.1) (MYOPHOSPHORYLASE). [Source:SWISSPROT;Acc:P11217]"	0.0229997	0.0845876	0.27190392	PYGM	
525	"GLYCOGEN PHOSPHORYLASE, BRAIN FORM (EC 2.4.1.1). [Source:SWISSPROT;Acc:P11216]"	0.0231429	0.0851144	0.271903462	PYGB	
526	MYOSIN XV (UNCONVENTIONAL MYOSIN-15). [Source:SWISSPROT;Acc:Q9UKN7]	0.0249116	0.0916194	0.271903112	MYO15A	
527	"GLYCOGEN PHOSPHORYLASE, LIVER FORM (EC 2.4.1.1). [Source:SWISSPROT;Acc:P06737]"	0.0249116	0.0916194	0.271903112	PYGL	
528	"PROTEIN PHOSPHATASE 1, REGULATORY (INHIBITOR) SUBUNIT 12B ISOFORM A; MYOSIN PHOSPHATASE REGULATORY SUBUNIT; MYOSIN PHOSPHATASE, TARGET SUBUNIT 2. [Source:RefSeq;Acc:NM_002481]"	0.309836	1.13987	0.271816962	PPP1R12B	
529	"PROTEIN PHOSPHATASE 1, REGULATORY (INHIBITOR) SUBUNIT 12A; MYOSIN PHOSPHATASE, TARGET SUBUNIT 1. [Source:RefSeq;Acc:NM_002480]"	0.253813	0.933978	0.271754795	PPP1R12A	
530		0.260139	0.957852	0.271585798	RBM24	
531	RNA-BINDING REGION CONTAINING PROTEIN 1 (HSRNASEB) (SSDNA BINDING PROTEIN SEB4) (CLL-ASSOCIATED ANTIGEN KW-5). [Source:SWISSPROT;Acc:Q9H0Z9]	0.216511	0.797256	0.271570236	RBM38	
532	"KARYOPHERIN BETA 2B, TRANSPORTIN; IMPORTIN 3. [Source:RefSeq;Acc:NM_013433]"	0.404881	1.49189	0.271387971	TNPO2	
533	SMALL NUCLEAR RIBONUCLEOPROTEIN F (SNRNP-F) (SM PROTEIN F) (SM-F) (SMF). [Source:SWISSPROT;Acc:Q15356]	0.232461	0.856628	0.271367501	SNRPF	
534	SMALL NUCLEAR RIBONUCLEOPROTEIN E (SNRNP-E) (SM PROTEIN E) (SM-E) (SME). [Source:SWISSPROT;Acc:P08578]	0.0399967	0.14739	0.271366443		
535	IMPORTIN BETA-2 SUBUNIT (KARYOPHERIN BETA-2 SUBUNIT) (TRANSPORTIN) (M9 REGION INTERACTION PROTEIN) (MIP). [Source:SWISSPROT;Acc:Q92973]	0.443276	1.63446	0.271206392	TNPO1	
536	BROMODOMAIN-CONTAINING PROTEIN 3 (RING3-LIKE PROTEIN). [Source:SWISSPROT;Acc:Q15059]	0.122154	0.450566	0.271112334	BRD3	
537	BROMODOMAIN-CONTAINING PROTEIN 2 (RING3 PROTEIN) (O27.1.1). [Source:SWISSPROT;Acc:P25440]	0.105783	0.390223	0.271083457	BRD2	
538	BROMODOMAIN-CONTAINING PROTEIN 4 (HUNK1 PROTEIN). [Source:SWISSPROT;Acc:O60885]	0.144761	0.534019	0.27107837	BRD4	
539		0.0778103	0.28704	0.271078247	SRBD1	
540		0.0358609	0.13229	0.271077935	LRRC4B	
541	NAG14 PROTEIN. [Source:RefSeq;Acc:NM_022143]	0.0376313	0.138821	0.271077863	LRRC4	
542	PROTEIN REGULATOR OF CYTOKINESIS 1; PROTEIN REGULATING CYTOKINESIS 1. [Source:RefSeq;Acc:NM_003981]	0.152328	0.561935	0.271077616		
543		0.0431799	0.15929	0.27107728	LRRC4C	
544	TESTIS-SPECIFIC BROMODOMAIN PROTEIN. [Source:RefSeq;Acc:NM_001726]	0.0996239	0.36752	0.27107069	BRDT	
545	QUAKING ISOFORM 6. [Source:SPTREMBL;Acc:Q9P0X9]	0.59995	2.2133	0.271065829	QKI	
546	ABHYDROLASE DOMAIN CONTAINING PROTEIN 2 (PROTEIN PHPS1-2). [Source:SWISSPROT;Acc:P08910]	0.0497647	0.183589	0.271065805	ABHD2	
547	"CUG TRIPLET REPEAT, RNA BINDING PROTEIN 2; ELAV-TYPE RNA-BINDING PROTEIN; CUG TRIPLET REPEAT,RNA-BINDING PROTEIN 2; CUG TRIPLET REPEAT, RNA-BINDING PROTEIN 2; NEUROBLASTOMA APOPTOSIS-RELATED RNA-BINDING PROTEIN. [Source:RefSeq;Acc:NM_006561]"	0.24526	0.905006	0.271003728	CUGBP2	
548	CUG TRIPLET REPEAT RNA-BINDING PROTEIN 1 (CUG-BP1) (RNA-BINDING PROTEIN BRUNOL-2) (DEADENYLATION FACTOR CUG-BP) (50 KDA NUCLEAR POLYADENYLATED RNA-BINDING PROTEIN) (EDEN-BP). [Source:SWISSPROT;Acc:Q92879]	0.267337	0.986471	0.271003405	CUGBP1	
549	SH3 DOMAIN-BINDING GLUTAMIC ACID-RICH PROTEIN (SH3BGR PROTEIN) (21- GLUTAMIC ACID-RICH PROTEIN) (21-GARP). [Source:SWISSPROT;Acc:P55822]	0.046789	0.172653	0.271000214	SH3BGR	
550	LATS HOMOLOG 1. [Source:RefSeq;Acc:NM_004690]	0.046789	0.172653	0.271000214	LATS1	

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/