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.

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

Rank Gene description measured expected final Hugo

Results: HTML CSV LaTeX

Showing element 1608 to 1657 of 3206 in total

Rank	description	measured	expected	final	Hugo	
1608	KATANIN P80 SUBUNIT B 1; KATANIN (80 KDA); KATANIN P80 (WD40-CONTAINING) SUBUNIT B 1. [Source:RefSeq;Acc:NM_005886]	0.0440508	0.183648	0.239865395	KATNB1	
1609	KATANIN P60 SUBUNIT A 1. [Source:RefSeq;Acc:NM_007044]	0.154124	0.64258	0.239851847	KATNA1	
1610	UBIQUITIN-CONJUGATING ENZYME E2 VARIANT 1 ISOFORM B; DNA-BINDING PROTEIN. [Source:RefSeq;Acc:NM_003349]	0.298042	1.24282	0.239811075	TMEM189	
1611	UTP--GLUCOSE-1-PHOSPHATE URIDYLYLTRANSFERASE 2 (EC 2.7.7.9) (UDP- GLUCOSE PYROPHOSPHORYLASE 2) (UDPGP 2) (UGPASE 2). [Source:SWISSPROT;Acc:Q16851]	0.203313	0.847819	0.239807081	UGP2	
1612	"UBIQUITIN-CONJUGATING ENZYME E2 VARIANT 2; 1 ALPHA,25-DIHYDROXYVITAMIN D3-INDUCIBLE; ENTEROCYTE DIFFERENTIATION PROMOTING FACTOR; METHYL METHANESULFONATE SENSITIVE 2, S. CEREVISIAE, HOMOLOG OF. [Source:RefSeq;Acc:NM_003350]"	0.274194	1.14341	0.239803745	UBE2V2	
1613	MITOCHONDRIAL RIBOSOMAL PROTEIN L30 ISOFORM A. [Source:RefSeq;Acc:NM_145212]	0.0388254	0.161954	0.239731035	MRPL30	
1614	26S PROTEASE REGULATORY SUBUNIT S10B (PROTEASOME SUBUNIT P42) (P44) (CONSERVED ATPASE DOMAIN PROTEIN 44) (CADP44). [Source:SWISSPROT;Acc:Q92524]	1.19046	4.96583	0.239730317	PSMC6	
1615		0.153801	0.641812	0.239635594	C20orf11	
1616		0.0384502	0.160453	0.239635283	MAEA	
1617		0.0384502	0.160453	0.239635283	RMND5A	
1618	ACID CERAMIDASE PRECURSOR (EC 3.5.1.23) (ACYLSPHINGOSINE DEACYLASE) (N-ACYLSPHINGOSINE AMIDOHYDROLASE) (AC) (PUTATIVE 32 KDA HEART PROTEIN) (PHP32). [Source:SWISSPROT;Acc:Q13510]	0.083902	0.35015	0.239617307	ASAH1	
1619	OLIGOPHRENIN 1. [Source:SWISSPROT;Acc:O60890]	0.0153184	0.063934	0.239597084	OPHN1	
1620	SENESCENCE MARKER PROTEIN-30 (SMP-30) (REGUCALCIN) (RC). [Source:SWISSPROT;Acc:Q15493]	0.0724203	0.302259	0.239596836	RGN	
1621	"CYTOCHROME C1, HEME PROTEIN, MITOCHONDRIAL PRECURSOR (CYTOCHROME C-1). [Source:SWISSPROT;Acc:P08574]"	0.150184	0.62682	0.239596694	CYC1	
1622	OLIGOPHRENIN-1 LIKE PROTEIN (GTPASE REGULATOR ASSOCIATED WITH FOCAL ADHESION KINASE). [Source:SWISSPROT;Acc:Q9UNA1]	0.0203871	0.0850893	0.239596518	ARHGAP26	
1623		0.0163276	0.0681463	0.23959628	ARHGAP10	
1624	CAMP-DEPENDENT PROTEIN KINASE TYPE II-BETA REGULATORY CHAIN. [Source:SWISSPROT;Acc:P31323]	0.337407	1.40952	0.239377235	PRKAR2B	
1625	PROTEIN KINASE PKX1 (EC 2.7.1.-). [Source:SWISSPROT;Acc:P51817]	0.143332	0.598798	0.239366197	PRKX	
1626	"CAMP-DEPENDENT PROTEIN KINASE, GAMMA-CATALYTIC SUBUNIT (EC 2.7.1.37) (PKA C-GAMMA). [Source:SWISSPROT;Acc:P22612]"	0.190544	0.796037	0.239365758	PRKACG	
1627	"CAMP-DEPENDENT PROTEIN KINASE, BETA-CATALYTIC SUBUNIT (EC 2.7.1.37) (PKA C-BETA). [Source:SWISSPROT;Acc:P22694]"	0.210706	0.880269	0.239365467	PRKACB	
1628	"CAMP-DEPENDENT PROTEIN KINASE, ALPHA-CATALYTIC SUBUNIT (EC 2.7.1.37) (PKA C-ALPHA). [Source:SWISSPROT;Acc:P17612]"	0.210706	0.880269	0.239365467	PRKACA	
1629	CAMP-DEPENDENT PROTEIN KINASE TYPE II-ALPHA REGULATORY CHAIN. [Source:SWISSPROT;Acc:P13861]	0.392337	1.63914	0.239355394	PRKAR2A	
1630		0.132038	0.551746	0.239309392	PHLPPL	
1631		0.167352	0.699345	0.2392982	PHLPP	
1632	TRIPARTITE MOTIF PROTEIN 2. [Source:SWISSPROT;Acc:Q9C040]	0.285075	1.19135	0.239287363	TRIM2	
1633		0.938982	3.92552	0.239199393	KIAA0368	
1634	INOSITOL-1(OR 4)-MONOPHOSPHATASE 2 (EC 3.1.3.25) (IMPASE 2) (IMP 2) (INOSITOL MONOPHOSPHATASE 2) (MYO-INOSITOL MONOPHOSPHATASE A2). [Source:SWISSPROT;Acc:O14732]	0.0919591	0.384447	0.239198381	IMPA2	
1635	INOSITOL-1(OR 4)-MONOPHOSPHATASE (EC 3.1.3.25) (IMPASE) (IMP) (INOSITOL MONOPHOSPHATASE) (LITHIUM-SENSITIVE MYO-INOSITOL MONOPHOSPHATASE A1). [Source:SWISSPROT;Acc:P29218]	0.110487	0.461922	0.239189733	IMPA1	
1636	MITOTIC CHECKPOINT PROTEIN BUB3. [Source:SWISSPROT;Acc:O43684]	0.153821	0.64312	0.239179313	BUB3	
1637	ZINC FINGER PROTEIN 207. [Source:SWISSPROT;Acc:O43670]	0.0769103	0.32156	0.239178691	ZNF207	
1638	26S PROTEASE REGULATORY SUBUNIT 6A (TAT-BINDING PROTEIN 1) (TBP-1) (PROTEASOME SUBUNIT P50). [Source:SWISSPROT;Acc:P17980]	0.766353	3.20427	0.239166175	PSMC3	
1639	26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 7 (26S PROTEASOME REGULATORY SUBUNIT S12) (PROTEASOME SUBUNIT P40) (MOV34 PROTEIN HOMOLOG). [Source:SWISSPROT;Acc:P51665]	0.790323	3.30538	0.239102009	PSMD7	
1640	ALPHA-FETOPROTEIN ENHANCER BINDING PROTEIN (AT MOTIF-BINDING FACTOR) (AT-BINDING TRANSCRIPTION FACTOR 1). [Source:SWISSPROT;Acc:Q15911]	0.0721691	0.301896	0.239052853	ZFHX3	
1641	UV EXCISION REPAIR PROTEIN RAD23 HOMOLOG A (HHR23A). [Source:SWISSPROT;Acc:P54725]	0.101079	0.422881	0.23902469	RAD23A	
1642		0.0488461	0.204356	0.239024545		
1643		0.0624093	0.2611	0.239024512	DDI1	
1644	26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 4 (26S PROTEASOME REGULATORY SUBUNIT S5A) (RPN10) (MULTIUBIQUITIN CHAIN BINDING PROTEIN) (ANTISECRETORY FACTOR-1) (AF) (ASF). [Source:SWISSPROT;Acc:P55036]	1.26742	5.30247	0.239024455	PSMD4	
1645	UV EXCISION REPAIR PROTEIN RAD23 HOMOLOG B (HHR23B) (XP-C REPAIR COMPLEMENTING COMPLEX 58 KDA PROTEIN) (P58). [Source:SWISSPROT;Acc:P54727]	0.122909	0.514211	0.239024447	RAD23B	
1646	MYOSIN VI. [Source:SWISSPROT;Acc:Q9UM54]	0.050323	0.210535	0.23902439		
1647		0.0275762	0.11537	0.23902401		
1648	INOSITOL POLYPHOSPHATE 5-PHOSPHATASE OCRL-1 (EC 3.1.3.36) (LOWE'S OCULOCEREBRORENAL SYNDROME PROTEIN). [Source:SWISSPROT;Acc:Q01968]	0.0555683	0.23248	0.239024002	OCRL	
1649		0.352885	1.47667	0.238973501	COQ5	
1650	"CHAPERONE-ACTIVITY OF BC1 COMPLEX-LIKE, MITOCHONDRIAL PRECURSOR (CHAPERONE-ABC1-LIKE). [Source:SWISSPROT;Acc:Q8NI60]"	0.0340138	0.142333	0.238973393	CABC1	
1651	AARF DOMAIN CONTAINING KINASE 1. [Source:RefSeq;Acc:NM_020421]	0.0340138	0.142333	0.238973393	ADCK1	
1652	AARF DOMAIN CONTAINING KINASE 2; PUTATIVE UBIQUINONE BIOSYNTHESIS PROTEIN AARF. [Source:RefSeq;Acc:NM_052853]	0.0340138	0.142333	0.238973393	ADCK2	
1653	AARF DOMAIN CONTAINING KINASE 4. [Source:RefSeq;Acc:NM_024876]	0.0274831	0.115005	0.238973088	ADCK4	
1654	26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 13 (26S PROTEASOME REGULATORY SUBUNIT S11) (26S PROTEASOME REGULATORY SUBUNIT P40.5). [Source:SWISSPROT;Acc:Q9UNM6]	0.75685	3.16764	0.238931823	PSMD13	
1655	APURINIC/APYRIMIDINIC ENDONUCLEASE 2; APURINIC/APYRIMIDINIC ENDONUCLEASE-LIKE 2; APEX NUCLEASE-LIKE 2. [Source:RefSeq;Acc:NM_014481]	0.0730689	0.305877	0.238883277	APEX2	
1656	COPPER-TRANSPORTING ATPASE 1 (EC 3.6.3.4) (COPPER PUMP 1) (MENKES DISEASE-ASSOCIATED PROTEIN). [Source:SWISSPROT;Acc:Q04656]	0.0806616	0.337708	0.238850131	ATP7A	
1657	CYCLIN M2; ANCIENT CONSERVED DOMAIN PROTEIN 2. [Source:RefSeq;Acc:NM_017649]	0.317455	1.3291	0.238849597	CNNM2	

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/