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 1302 to 1351 of 3206 in total

Rank	description	measured	expected	final	Hugo	
1302	TRANSLATION INITIATION FACTOR EIF-2B GAMMA SUBUNIT (EIF-2B GDP-GTP EXCHANGE FACTOR). [Source:SWISSPROT;Acc:Q9NR50]	0.473798	1.92792	0.245756048	EIF2B3	
1303	TRANSLATION INITIATION FACTOR EIF-2B EPSILON SUBUNIT (EIF-2B GDP-GTP EXCHANGE FACTOR). [Source:SWISSPROT;Acc:Q13144]	0.473798	1.92792	0.245756048	EIF2B5	
1304	RAD9 HOMOLOG; CELL CYCLE CHECKPOINT CONTROL PROTEIN; RAD9 HOMOLOG (S. POMBE). [Source:RefSeq;Acc:NM_004584]	0.0763771	0.310798	0.245745146	RAD9A	
1305	"PROLYL 4-HYDROXYLASE ALPHA-2 SUBUNIT PRECURSOR (EC 1.14.11.2) (4-PH ALPHA-2) (PROCOLLAGEN-PROLINE,2-OXOGLUTARATE-4-DIOXYGENASE ALPHA-2 SUBUNIT). [Source:SWISSPROT;Acc:O15460]"	0.0266534	0.108468	0.245725928	P4HA2	
1306	HYALURONAN BINDING PROTEIN 4; INTRACELLULAR ANTIGEN DETECTED BY MONOCLONAL ANTIBODY KI-1; INTRACELLULAR HYALURONAN-BINDING PROTEIN; CHROMODOMAIN HELICASE DNA BINDING PROTEIN 3 INTERACTING PROTEIN. [Source:RefSeq;Acc:NM_014282]	0.0335632	0.136588	0.245725832	HABP4	
1307	PROTEIN DISULFIDE ISOMERASE PRECURSOR (PDI) (EC 5.3.4.1) (PROLYL 4- HYDROXYLASE BETA SUBUNIT) (CELLULAR THYROID HORMONE BINDING PROTEIN) (P55). [Source:SWISSPROT;Acc:P07237]	0.143784	0.58514	0.245725809	P4HB	
1308	RAD1 HOMOLOG ISOFORM 1; EXONUCLEASE HOMOLOG RAD1; CELL CYCLE CHECKPOINT PROTEIN RAD1 A/B; RAD1-LIKE PROTEIN; CELL CYCLE CHECKPOINT PROTEIN HRAD1; DNA REPAIR EXONUCLEASE (REC1); DNA REPAIR PROTEIN RAD1; RAD1-LIKE DNA DAMAGE CHECKPOINT PROTEIN. [Source:RefS	0.874478	3.55876	0.245725477	RAD1	
1309	HOMEOBOX PROSPERO-LIKE PROTEIN PROX1 (PROX 1). [Source:SWISSPROT;Acc:Q92786]	0.0419409	0.170682	0.245725384	PROX1	
1310	HUS1 CHECKPOINT PROTEIN; HUS1 (S. POMBE) CHECKPOINT HOMOLOG; HUS1+-LIKE PROTEIN. [Source:RefSeq;Acc:NM_004507]	0.201117	0.818463	0.245725219	HUS1	
1311		0.0417836	0.170042	0.245725174	SERBP1	
1312	"3-HYDROXYANTHRANILATE 3,4-DIOXYGENASE (EC 1.13.11.6) (3-HAO) (3-HYDROXYANTHRANILIC ACID DIOXYGENASE) (3-HYDROXYANTHRANILATE OXYGENASE). [Source:SWISSPROT;Acc:P46952]"	0.0418885	0.170469	0.245725029	HAAO	
1313	ZINC FINGER PROTEIN-LIKE 1; ZINC-FINGER PROTEIN IN MEN1 REGION. [Source:RefSeq;Acc:NM_006782]	0.0418885	0.170469	0.245725029	ZFPL1	
1314	"PROLYL 4-HYDROXYLASE ALPHA-1 SUBUNIT PRECURSOR (EC 1.14.11.2) (4-PH ALPHA-1) (PROCOLLAGEN-PROLINE,2-OXOGLUTARATE-4-DIOXYGENASE ALPHA-1 SUBUNIT). [Source:SWISSPROT;Acc:P13674]"	0.0333011	0.135522	0.245724679	P4HA1	
1315	HYDROXYACID OXIDASE 1 (EC 1.1.3.15) (HAOX1) (GLYCOLATE OXIDASE) (GOX). [Source:SWISSPROT;Acc:Q9UJM8]	0.517862	2.1077	0.245700052	HAO1	
1316	TGF BETA-INDUCIBLE NUCLEAR PROTEIN 1; HAIRY CELL LEUKEMIA PROTEIN 1. [Source:RefSeq;Acc:NM_014886]	0.448528	1.82552	0.24569876		
1317	ATP-DEPENDENT RNA HELICASE MGC2835; ATP-DEPENDENT RNA HELICASE; APOPTOSIS RELATED PROTEIN APR-5; DEAD BOX HELICASE 97 KDA. [Source:RefSeq;Acc:NM_024072]	0.517911	2.10824	0.245660361	DDX54	
1318		0.479433	1.95163	0.245657732	WDR74	
1319		0.269894	1.09872	0.245644022	ARD1B	
1320	THIOREDOXIN DOMAIN-CONTAINING 2; SPERM-SPECIFIC THIOREDOXIN; THIOREDOXIN DOMAIN-CONTAINING 2 (SPERMATOZOA). [Source:RefSeq;Acc:NM_032243]	0.0247366	0.100732	0.245568439	TXNDC2	
1321	THIOREDOXIN (ATL-DERIVED FACTOR) (ADF) (SURFACE ASSOCIATED SULPHYDRYL PROTEIN) (SASP). [Source:SWISSPROT;Acc:P10599]	0.0297584	0.121182	0.245567824	TXN	
1322	60S ACIDIC RIBOSOMAL PROTEIN P1. [Source:SWISSPROT;Acc:P05386]	0.310893	1.26602	0.245567211		
1323	CENTROMERE PROTEIN J; CENTROSOMAL P4.1-ASSOCIATED PROTEIN; LYST-INTERACTING PROTEIN LIP1; LAG-3-ASSOCIATED PROTEIN. [Source:RefSeq;Acc:NM_018451]	0.146257	0.595639	0.24554638	CENPJ	
1324	"28S RIBOSOMAL PROTEIN S26, MITOCHONDRIAL PRECURSOR (MRP-S26) (MRP- S13). [Source:SWISSPROT;Acc:Q9BYN8]"	0.0393961	0.160458	0.245522816	MRPS26	
1325		0.0393961	0.160458	0.245522816	CHCHD4	
1326	ENHANCER OF RUDIMENTARY HOMOLOG. [Source:SWISSPROT;Acc:Q14259]	0.271803	1.10704	0.245522294	ERH	
1327	WD-REPEAT PROTEIN 12 (YTM1 HOMOLOG). [Source:SWISSPROT;Acc:Q9GZL7]	0.829705	3.37944	0.245515529	WDR12	
1328	NIF3-LIKE PROTEIN 1 (AMYOTROPHIC LATERAL SCLEROSIS 2 CHROMOSOMAL REGION CANDIDATE GENE PROTEIN 1) (MY018 PROTEIN) (MDS015). [Source:SWISSPROT;Acc:Q9GZT8]	0.166892	0.679841	0.245486812		
1329	PROBABLE ATP-DEPENDENT 61 KDA NUCLEOLAR RNA HELICASE (DEAD-BOX PROTEIN 21). [Source:SWISSPROT;Acc:Q9NY93]	0.280718	1.14368	0.245451525	DDX56	
1330	SACCHAROMYCES CEREVISIAE NIP7P HOMOLOG. [Source:RefSeq;Acc:NM_016101]	0.455858	1.85732	0.245438589	NIP7	
1331	NNP-1 PROTEIN (NOVEL NUCLEAR PROTEIN 1) (NUCLEOLAR PROTEIN NOP52) (NOP52) (D21S2056E). [Source:SWISSPROT;Acc:P56182]	0.213008	0.867932	0.245420148	RRP1	
1332	NUCLEOLAR GTP-BINDING PROTEIN 1 (CHRONIC RENAL FAILURE GENE PROTEIN) (GTP-BINDING PROTEIN NGB). [Source:SWISSPROT;Acc:Q9BZE4]	0.872438	3.55541	0.245383233	GTPBP4	
1333	MYB-RELATED PROTEIN B (B-MYB). [Source:SWISSPROT;Acc:P10244]	0.102811	0.419099	0.245314353	MYBL2	
1334	AD24 PROTEIN. [Source:RefSeq;Acc:NM_022451]	0.290237	1.18321	0.24529627	NOC3L	
1335	SUPPRESSOR OF SWI4 1 HOMOLOG (SSF-1) (PETER PAN HOMOLOG). [Source:SWISSPROT;Acc:Q9NQ55]	0.0742746	0.302799	0.245293412	PPAN-P2RY11	
1336	CYCLIC-AMP-DEPENDENT TRANSCRIPTION FACTOR ATF-6 BETA (ACTIVATING TRANSCRIPTION FACTOR 6 BETA) (ATF6-BETA) (CAMP RESPONSIVE ELEMENT BINDING PROTEIN-LIKE 1) (CAMP RESPONSE ELEMENT BINDING PROTEIN-RELATED PROTEIN) (CREB-RP) (G13 PROTEIN). [Source:SWISSPROT;A	0.0331688	0.135226	0.245284191	CREBL1	
1337	DNA SEGMENT ON CHROMOSOME 6(UNIQUE) 2654 EXPRESSED SEQUENCE; DNA SEGMENT ON CHROMOSOME X (UNIQUE) 2654 EXPRESSED SEQUENCE. [Source:RefSeq;Acc:NM_012135]	0.0375954	0.153273	0.245283905	FAM50B	
1338	SFRS PROTEIN KINASE 2 ISOFORM B. [Source:RefSeq;Acc:NM_182691]	0.0349958	0.142675	0.245283336	SRPK2	
1339	GTP BINDING PROTEIN 2. [Source:RefSeq;Acc:NM_019096]	1.5466	6.30537	0.245282989	GTPBP2	
1340	SFRS PROTEIN KINASE 1; SR PROTEIN KINASE 1. [Source:RefSeq;Acc:NM_003137]	0.0417611	0.170257	0.24528272	SRPK1	
1341	XAP-5 PROTEIN (HXC-26 PROTEIN). [Source:SWISSPROT;Acc:Q14320]	0.0417611	0.170257	0.24528272	FAM50A	
1342	SERINE/THREONINE PROTEIN KINASE 23 (EC 2.7.1.37) (MUSCLE-SPECIFIC SERINE KINASE 1) (MSSK-1). [Source:SWISSPROT;Acc:Q9UPE1]	0.0417611	0.170257	0.24528272	SRPK3	
1343	CYCLIC-AMP-DEPENDENT TRANSCRIPTION FACTOR ATF-6 ALPHA (ACTIVATING TRANSCRIPTION FACTOR 6 ALPHA) (ATF6-ALPHA). [Source:SWISSPROT;Acc:P18850]	0.0417611	0.170257	0.24528272	ATF6	
1344	RAB3A INTERACTING PROTEIN ISOFORM ALPHA 1; RABIN3; SSX2 INTERACTING PROTEIN. [Source:RefSeq;Acc:NM_022456]	0.165502	0.674746	0.245280446	RAB3IP	
1345	PROBABLE RRNA PROCESSING PROTEIN EBP2 (EBNA1 BINDING PROTEIN 2) (NUCLEOLAR PROTEIN P40). [Source:SWISSPROT;Acc:Q99848]	0.271421	1.10693	0.245201594	EBNA1BP2	
1346	RAB3A INTERACTING PROTEIN (RABIN3)-LIKE 1. [Source:RefSeq;Acc:NM_013401]	0.197255	0.804471	0.245198397	RAB3IL1	
1347	WD REPEAT DOMAIN 26. [Source:RefSeq;Acc:NM_025160]	0.108431	0.442236	0.24518809	WDR26	
1348	J KAPPA-RECOMBINATION SIGNAL BINDING PROTEIN (RBP-J KAPPA). [Source:SWISSPROT;Acc:Q06330]	0.517438	2.11039	0.245185961	RBPJ	
1349	HUMAN IMMUNODEFICIENCY VIRUS TYPE I ENHANCER-BINDING PROTEIN 2 (HIV-EP2). [Source:SWISSPROT;Acc:P31629]	0.0401322	0.163681	0.245185452	HIVEP2	
1350	ZINC FINGER PROTEIN 40 (HUMAN IMMUNODEFICIENCY VIRUS TYPE I ENHANCER- BINDING PROTEIN 1) (HIV-EP1) (MAJOR HISTOCOMPATIBILITY COMPLEX BINDING PROTEIN 1) (MBP-1) (POSITIVE REGULATORY DOMAIN II BINDING FACTOR 1) (PRDII-BF1). [Source:SWISSPROT;Acc:P15822]	0.0471496	0.192302	0.245185177	HIVEP1	
1351	HUMAN IMMUNODEFICIENCY VIRUS TYPE I ENHANCER BINDING PROTEIN 3. [Source:RefSeq;Acc:NM_024503]	0.0391877	0.159829	0.245185167	HIVEP3	

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/