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 1502 to 1551 of 3206 in total

Rank	description	measured	expected	final	Hugo	
1502	"CIRHIN; TESTIS EXPRESSED GENE 292; CIRRHOSIS, AUTOSOMAL RECESSIVE 1A. [Source:RefSeq;Acc:NM_032830]"	0.588096	2.42296	0.242717998	CIRH1A	
1503	ZUOTIN RELATED FACTOR-1 (M-PHASE PHOSPHOPROTEIN 11). [Source:SWISSPROT;Acc:Q99543]	0.0271819	0.112006	0.242682535	ZRF1	
1504	GUANINE NUCLEOTIDE-BINDING PROTEIN BETA SUBUNIT-LIKE PROTEIN 12.3 (P205) (RECEPTOR OF ACTIVATED PROTEIN KINASE C 1) (RACK1) (RECEPTOR FOR ACTIVATED C KINASE). [Source:SWISSPROT;Acc:P25388]	0.112103	0.461933	0.24268238		
1505	PBK1 PROTEIN. [Source:SPTREMBL;Acc:O76021]	0.485772	2.00168	0.242682147	RSL1D1	
1506	WD-REPEAT PROTEIN BING4. [Source:SWISSPROT;Acc:O15213]	0.562114	2.31688	0.242616795	WDR46	
1507		0.511781	2.10953	0.242604277	NOC4L	
1508	PROBABLE RIBOSOME BIOGENESIS PROTEIN NEP1 (C2F PROTEIN). [Source:SWISSPROT;Acc:Q92979]	0.511781	2.10953	0.242604277	EMG1	
1509	EXOCYST COMPLEX COMPONENT SEC6. [Source:SWISSPROT;Acc:O60645]	0.0383868	0.158229	0.24260281	EXOC3	
1510		0.11516	0.474687	0.242601967	C19orf50	
1511		0.0256005	0.105559	0.242523139	NGDN	
1512	APOPTOSIS ANTAGONIZING TRANSCRIPTION FACTOR. [Source:RefSeq;Acc:NM_012138]	0.46077	1.89991	0.242522014	AATF	
1513		0.0884483	0.36491	0.242383875	ATPBD4	
1514		0.332106	1.37021	0.242375986	WDSOF1	
1515	KELCH-LIKE ECH-ASSOCIATED PROTEIN 1 (CYTOSOLIC INHIBITOR OF NRF2). [Source:SWISSPROT;Acc:Q14145]	0.0838767	0.346067	0.242371275	KEAP1	
1516	DNA REPLICATION LICENSING FACTOR MCM3 (DNA POLYMERASE ALPHA HOLOENZYME-ASSOCIATED PROTEIN P1) (RLF BETA SUBUNIT) (P102 PROTEIN) (P1-MCM3). [Source:SWISSPROT;Acc:P25205]	0.0279589	0.115356	0.242370575	MCM3	
1517	GLIA MATURATION FACTOR GAMMA (GMF-GAMMA). [Source:SWISSPROT;Acc:O60234]	0.0675774	0.278856	0.242337981	GMFG	
1518	SUPPRESSOR OF CYTOKINE SIGNALING 1 (SOCS-1) (JAK-BINDING PROTEIN) (JAB) (STAT INDUCED STAT INHIBITOR 1) (SSI-1) (TEC-INTERACTING PROTEIN 3) (TIP-3). [Source:SWISSPROT;Acc:O15524]	0.0338352	0.13962	0.242337774	SOCS1	
1519	FK506-BINDING PROTEIN 1A (EC 5.2.1.8) (PEPTIDYL-PROLYL CIS-TRANS ISOMERASE) (PPIASE) (ROTAMASE) (12 KDA FKBP) (FKBP-12) (IMMUNOPHILIN FKBP12). [Source:SWISSPROT;Acc:P20071]	0.0338352	0.13962	0.242337774	FKBP1A	
1520		0.161284	0.665535	0.242337368	PAN3	
1521	ASC-1 COMPLEX SUBUNIT P100. [Source:RefSeq;Acc:NM_032204]	0.0336999	0.139062	0.242337231	ASCC2	
1522		0.101184	0.417534	0.242337151	RBM22	
1523	NUCLEOLAR PROTEIN NOP56 (NUCLEOLAR PROTEIN 5A). [Source:SWISSPROT;Acc:O00567]	0.66215	2.73239	0.242333635	NOL5A	
1524	RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE M1 CHAIN (EC 1.17.4.1) (RIBONUCLEOTIDE REDUCTASE LARGE CHAIN). [Source:SWISSPROT;Acc:P23921]	0.123369	0.509096	0.242329541	RRM1	
1525	KINESIN-LIKE PROTEIN KIF3B (MICROTUBULE PLUS END-DIRECTED KINESIN MOTOR 3B) (HH0048). [Source:SWISSPROT;Acc:O15066]	0.105382	0.43488	0.242324319	KIF3B	
1526	DOWN-REGULATED IN METASTASIS. [Source:RefSeq;Acc:NM_014503]	1.17672	4.8561	0.242317909	UTP20	
1527	"RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 3; RHOGEF PROTEIN; 59.8 KDA PROTEIN; EXCHANGE FACTOR FOUND IN PLATELETS AND LEUKEMIC AND NEURONAL TISSUES, XPLN. [Source:RefSeq;Acc:NM_019555]"	0.0223435	0.0922076	0.242317336	ARHGEF3	
1528	NEUROEPITHELIAL CELL TRANSFORMING GENE 1; GUANINE NUCLEOTIDE REGULATORY PROTEIN (ONCOGENE); RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR (GEF) 8. [Source:RefSeq;Acc:NM_005863]	0.0256013	0.105652	0.24231723	NET1	
1529	KINESIN-LIKE PROTEIN KIF3C. [Source:SWISSPROT;Acc:O14782]	0.0849863	0.350755	0.242295334	KIF3C	
1530	EUKARYOTIC TRANSLATION INITIATION FACTOR 6 (EIF-6) (B4 INTEGRIN INTERACTOR) (CAB) (P27(BBP)) (B(2)GCN HOMOLOG). [Source:SWISSPROT;Acc:P56537]	0.850503	3.51033	0.242285768	EIF6	
1531	ATP-DEPENDENT RNA HELICASE ROK1; ATP-DEPENDENT RNA HELICASE. [Source:RefSeq;Acc:NM_007010]	0.0764864	0.315775	0.242218035	DDX52	
1532	NIN ONE BINDING PROTEIN; ADENOCARCINOMA ANTIGEN RECOGNIZED BY T LYMPHOCYTES 4. [Source:RefSeq;Acc:NM_014062]	0.0805704	0.332683	0.2421837	NOB1	
1533	NADH-UBIQUINONE OXIDOREDUCTASE PDSW SUBUNIT (EC 1.6.5.3) (EC 1.6.99.3) (COMPLEX I-PDSW) (CI-PDSW). [Source:SWISSPROT;Acc:O96000]	0.322293	1.3313	0.242088936	NDUFB10	
1534	IRON-RESPONSIVE ELEMENT BINDING PROTEIN 1 (IRE-BP 1) (IRON REGULATORY PROTEIN 1) (IRP1) (FERRITIN REPRESSOR PROTEIN) (ACONITATE HYDRATASE) (EC 4.2.1.3) (CITRATE HYDRO-LYASE) (ACONITASE). [Source:SWISSPROT;Acc:P21399]	0.195279	0.806892	0.242013801	ACO1	
1535	UBIQUITIN-CONJUGATING ENZYME E2 N (EC 6.3.2.19) (UBIQUITIN-PROTEIN LIGASE N) (UBIQUITIN CARRIER PROTEIN N) (UBC13) (BENDLESS-LIKE UBIQUITIN CONJUGATING ENZYME). [Source:SWISSPROT;Acc:Q16781]	0.132301	0.546679	0.242008564	UBE2N	
1536	"5-FORMYLTETRAHYDROFOLATE CYCLO-LIGASE (EC 6.3.3.2) (5,10-METHENYL- TETRAHYDROFOLATE SYNTHETASE) (METHENYL-THF SYNTHETASE) (MTHFS). [Source:SWISSPROT;Acc:P49914]"	0.0691225	0.285651	0.241982349	MTHFS	
1537	"INHIBITOR OF GROWTH FAMILY, MEMBER 1; INHIBITOR OF GROWTH 1. [Source:RefSeq;Acc:NM_005537]"	0.111297	0.459981	0.241959994	ING1	
1538	TRANSLATION INITIATION FACTOR EIF-2B DELTA SUBUNIT (EIF-2B GDP-GTP EXCHANGE FACTOR). [Source:SWISSPROT;Acc:Q9UI10]	0.287772	1.18956	0.241914658	EIF2B4	
1539	HISTONE H3.3 (H3.A) (H3.B) (H3.3Q). [Source:SWISSPROT;Acc:P06351]	0.21933	0.906671	0.241906932		
1540	DJ1099D15.1 (PUTATIVE DNAJ PROTEIN). [Source:SPTREMBL;Acc:Q9H4J9]	0.0214576	0.0887019	0.241906881		
1541	"DNA-DIRECTED RNA POLYMERASES I, II, AND III 17.1 KDA POLYPEPTIDE (EC 2.7.7.6) (RPB17) (RPB8) (RPABC3). [Source:SWISSPROT;Acc:P52434]"	0.345751	1.42971	0.241832959	POLR2H	
1542	NUCLEAR FACTOR NF-KAPPA-B P100/P49 SUBUNITS (H2TF1) (ONCOGENE LYT-10) (LYT10) [CONTAINS: NUCLEAR FACTOR NF-KAPPA-B P52 SUBUNIT]. [Source:SWISSPROT;Acc:Q00653]	0.415216	1.71705	0.2418194	NFKB2	
1543	NF-KAPPAB INHIBITOR BETA (NF-KAPPA-BIB) (I-KAPPA-B-BETA) (IKAPPABBETA) (IKB-BETA) (IKB-B) (THYROID RECEPTOR INTERACTING PROTEIN 9) (TR- INTERACTING PROTEIN 9). [Source:SWISSPROT;Acc:Q15653]	0.414708	1.71495	0.241819295	NFKBIB	
1544	NUCLEAR FACTOR NF-KAPPA-B P105 SUBUNIT (DNA-BINDING FACTOR KBF1) (EBP- 1) [CONTAINS: NUCLEAR FACTOR NF-KAPPA-B P50 SUBUNIT]. [Source:SWISSPROT;Acc:P19838]	0.415555	1.71846	0.241818256	NFKB1	
1545	B-CELL LYMPHOMA 3-ENCODED PROTEIN (BCL-3 PROTEIN). [Source:SWISSPROT;Acc:P20749]	0.424367	1.75491	0.241816959	BCL3	
1546	"INHIBITOR OF GROWTH FAMILY, MEMBER 1-LIKE; INHIBITOR OF GROWTH 1-LIKE. [Source:RefSeq;Acc:NM_001564]"	0.132686	0.548709	0.241814878	ING2	
1547	NF-KAPPAB INHIBITOR EPSILON (NF-KAPPA-BIE) (I-KAPPA-B-EPSILON) (IKAPPABEPSILON) (IKB-EPSILON) (IKBE). [Source:SWISSPROT;Acc:O00221]	0.56383	2.33188	0.24179203	NFKBIE	
1548	VACUOLAR ATP SYNTHASE SUBUNIT D (EC 3.6.3.14) (V-ATPASE D SUBUNIT) (VACUOLAR PROTON PUMP D SUBUNIT) (V-ATPASE AC39 SUBUNIT) (V-ATPASE 40 KDA ACCESSORY PROTEIN) (P39) (32 KDA ACCESSORY PROTEIN). [Source:SWISSPROT;Acc:P12953]	0.584458	2.4172	0.241791329	ATP6V0D1	
1549	ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 4. [Source:SWISSPROT;Acc:P40617]	0.0296714	0.122715	0.241791142	ARL4A	
1550	ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 7 (ADP-RIBOSYLATION FACTOR-LIKE PROTEIN LAK). [Source:SWISSPROT;Acc:P56559]	0.0364961	0.150941	0.241790501		
1551		0.129986	0.53787	0.241668061	PDRG1	

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/