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 902 to 951 of 3206 in total 
Rank	description	measured	expected	final	Hugo	
902	LIMBIC SYSTEM-ASSOCIATED MEMBRANE PROTEIN PRECURSOR (LSAMP). [Source:SWISSPROT;Acc:Q13449]	0.128336	0.494891	0.25932175	LSAMP	
903	OPIOID BINDING PROTEIN/CELL ADHESION MOLECULE PRECURSOR (OBCAM) (OPIOID-BINDING CELL ADHESION MOLECULE) (OPCML). [Source:SWISSPROT;Acc:Q14982]	0.145116	0.560999	0.258674258	OPCML	
904	PEPTIDYLPROLYL ISOMERASE-LIKE 4; CYCLOPHILIN-TYPE PEPTIDYL-PROLYL CIS-TRANS ISOMERASE; PPIASE; SEROLOGICALLY DEFINED BREAST CANCER ANTIGEN NY-BR-18. [Source:RefSeq;Acc:NM_139126]	0.227308	0.879442	0.258468438	PPIL4	
905	SIMILAR TO GLUCOSAMINE-PHOSPHATE N-ACETYLTRANSFERASE (HYPOTHETICAL PROTEIN FLJ33258). [Source:SPTREMBL;Acc:Q96EK6]	0.29051	1.12415	0.258426367	GNPNAT1	
906	DELTA-INTERACTING PROTEIN A (HEPATITIS DELTA ANTIGEN INTERACTING PROTEIN A). [Source:SWISSPROT;Acc:Q15834]	0.24009	0.929064	0.258421379	CCDC85B	
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	NR6A1	
908	SEROLOGICALLY DEFINED COLON CANCER ANTIGEN 16. [Source:RefSeq;Acc:NM_006649]	0.0771492	0.298726	0.258260747	UTP14A	
909	NEUROTRIMIN PRECURSOR (HNT). [Source:SWISSPROT;Acc:Q9P121]	0.159907	0.619267	0.258219799		
910		0.233873	0.906259	0.258064196	CCDC85A	
911	LYMPHOID ENHANCER BINDING FACTOR 1 (LEF-1) (T CELL-SPECIFIC TRANSCRIPTION FACTOR 1-ALPHA) (TCF1-ALPHA). [Source:SWISSPROT;Acc:Q9UJU2]	0.427985	1.6585	0.258055472	LEF1	
912		0.0349547	0.135465	0.258034917	SLC37A2	
913	GLYCEROL-3-PHOSPHATE TRANSPORTER (G-3-P TRANSPORTER) (G-3-P PERMEASE). [Source:SWISSPROT;Acc:P57057]	0.0275088	0.106609	0.2580345	SLC37A1	
914	"PROLINE OXIDASE, MITOCHONDRIAL PRECURSOR (EC 1.5.3.-) (PROLINE DEHYDROGENASE). [Source:SWISSPROT;Acc:O43272]"	0.198381	0.768816	0.258034432	PRODH	
915	INTERLEUKIN-4 INDUCED PROTEIN 1 PRECURSOR (FIG-1 PROTEIN). [Source:SWISSPROT;Acc:Q96RQ9]	0.19466	0.754632	0.257953546	IL4I1	
916	VACUOLAR PROTEIN SORTING 33A (HVPS33A). [Source:SWISSPROT;Acc:Q96AX1]	0.132652	0.514271	0.257941824	VPS33A	
917	VACUOLAR PROTEIN SORTING 33B (HVPS33B). [Source:SWISSPROT;Acc:Q9H267]	0.104198	0.40396	0.25794138	VPS33B	
918	VACUOLAR PROTEIN SORTING 11 (HVPS11) (PP3476). [Source:SWISSPROT;Acc:Q9H270]	0.167384	0.648924	0.257940837	VPS11	
919	RAL GUANINE NUCLEOTIDE EXCHANGE FACTOR RALGPS1A. [Source:RefSeq;Acc:NM_014636]	0.0509651	0.197588	0.257936211	RALGPS1	
920	RAL-A EXCHANGE FACTOR RALGPS2. [Source:RefSeq;Acc:NM_152663]	0.040067	0.155337	0.257935971	RALGPS2	
921	STIP1 HOMOLOGY AND U-BOX CONTAINING PROTEIN 1; SEROLOGICALLY DEFINED COLON CANCER ANTIGEN 7; CARBOXY TERMINUS OF HSP70P-INTERACTING PROTEIN; HEAT SHOCK PROTEIN A BINDING PROTEIN 2 (C-TERMINAL). [Source:RefSeq;Acc:NM_005861]	0.419455	1.6262	0.257935678	STUB1	
922	ALPHA CRYSTALLIN C CHAIN (SMALL STRESS PROTEIN-LIKE PROTEIN HSP22) (E2IG1) (PROTEIN KINASE H11). [Source:SWISSPROT;Acc:Q9UJY1]	0.208436	0.808729	0.257732813	HSPB8	
923	HEAT SHOCK 27 KDA PROTEIN (HSP 27) (STRESS-RESPONSIVE PROTEIN 27) (SRP27) (ESTROGEN-REGULATED 24 KDA PROTEIN) (28 KDA HEAT SHOCK PROTEIN). [Source:SWISSPROT;Acc:P04792]	0.28007	1.08675	0.257713366	HSPB1	
924	FATTY ACID DESATURASE 1; LINOLEOYL-COA DESATURASE (DELTA-6-DESATURASE)-LIKE 1; DELTA-5 DESATURASE; DELTA-5 FATTY ACID DESATURASE. [Source:RefSeq;Acc:NM_013402]	0.0378274	0.1468	0.257679837		
925	FATTY ACID DESATURASE 3; LINOLEOYL-COA DESATURASE (DELTA-6-DESATURASE)-LIKE 3; DELTA-6 FATTY ACID DESATURASE. [Source:RefSeq;Acc:NM_021727]	0.0325155	0.126186	0.25767914	FADS3	
926	GERANYLGERANYL TRANSFERASE TYPE I BETA SUBUNIT (EC 2.5.1.-) (TYPE I PROTEIN GERANYL-GERANYLTRANSFERASE BETA SUBUNIT) (GGTASE-I-BETA). [Source:SWISSPROT;Acc:P53609]	0.0378747	0.146984	0.257679067	PGGT1B	
927	MOTHERS AGAINST DECAPENTAPLEGIC HOMOLOG 4 (SMAD 4) (MOTHERS AGAINST DPP HOMOLOG 4) (DELETION TARGET IN PANCREATIC CARCINOMA 4) (HSMAD4). [Source:SWISSPROT;Acc:Q13485]	0.303187	1.17661	0.257678415	SMAD4	
928	FATTY ACID DESATURASE 2; LINOLEOYL-COA DESATURASE (DELTA-6-DESATURASE)-LIKE 2; DELTA-6 FATTY ACID DESATURASE. [Source:RefSeq;Acc:NM_004265]	0.0336801	0.130706	0.257678301	FADS2	
929	PROTEIN TRANSLATION FACTOR SUI1 HOMOLOG (SUI1ISO1). [Source:SWISSPROT;Acc:P41567]	0.546429	2.12125	0.257597643	EIF1	
930	DYNEIN LIGHT CHAIN 2. [Source:RefSeq;Acc:NM_080677]	0.266007	1.03319	0.257461841	DYNLL2	
931	SHORT COILED-COIL PROTEIN; SHORT COILED COIL PROTEIN. [Source:RefSeq;Acc:NM_032547]	0.0348108	0.135208	0.257461097	SCOC	
932	LIMKAIN BETA 2. [Source:RefSeq;Acc:NM_025140]	0.167087	0.649575	0.257225109	CCDC92	
933	ADENYLOSUCCINATE LYASE (EC 4.3.2.2) (ADENYLOSUCCINASE) (ASL) (ASASE). [Source:SWISSPROT;Acc:P30566]	0.289435	1.12698	0.256823546	ADSL	
934	CYCLIN C. [Source:SWISSPROT;Acc:P24863]	0.0849609	0.330921	0.256740733	CCNC	
935	PROTEIN TARA (TRIO-ASSOCIATED REPEAT ON ACTIN) (HRIHFB2122). [Source:SWISSPROT;Acc:Q9H2D6]	0.0598365	0.233092	0.256707652	TRIOBP	
936	RHO INTERACTING PROTEIN 3. [Source:RefSeq;Acc:NM_015134]	0.0739754	0.28817	0.256707499		
937	IMPORTIN ALPHA-6 SUBUNIT (KARYOPHERIN ALPHA-5 SUBUNIT). [Source:SWISSPROT;Acc:O15131]	1.37404	5.35803	0.256444999	KPNA6	
938	CHOLINE O-ACETYLTRANSFERASE (EC 2.3.1.6) (CHOACTASE) (CHOLINE ACETYLASE) (CHAT). [Source:SWISSPROT;Acc:P28329]	0.0510434	0.199072	0.256406727	CHAT	
939	YIP1 INTERACTING FACTOR HOMOLOG; YIP1P-INTERACTING FACTOR; PUTATIVE RAB5-INTERACTING PROTEIN; PUTATIVE TRANSMEMBRANE PROTEIN 54TMP. [Source:RefSeq;Acc:NM_020470]	0.121116	0.472359	0.256406674	YIF1A	
940	"METHYLMALONATE-SEMIALDEHYDE DEHYDROGENASE [ACYLATING], MITOCHONDRIAL PRECURSOR (EC 1.2.1.27) (MMSDH). [Source:SWISSPROT;Acc:Q02252]"	0.0637409	0.248593	0.256406657	ALDH6A1	
941	VOLTAGE-GATED POTASSIUM CHANNEL BETA-3 SUBUNIT (K+ CHANNEL BETA-3 SUBUNIT) (KV-BETA-3). [Source:SWISSPROT;Acc:O43448]	0.0570543	0.222515	0.256406534	KCNAB3	
942		0.0943614	0.368015	0.256406396	C1orf121	
943	AFLATOXIN B1 ALDEHYDE REDUCTASE 2 (EC 1.-.-.-) (AFB1-AR 2). [Source:SWISSPROT;Acc:O95154]	0.0645005	0.251556	0.256406128	AKR7A3	
944	ALPHA/BETA HYDROLASE DOMAIN CONTAINING PROTEIN 3; LUNG ALPHA/BETA HYDROLASE 3. [Source:RefSeq;Acc:NM_138340]	0.0204392	0.0797142	0.25640601	ABHD3	
945	AFLATOXIN B1 ALDEHYDE REDUCTASE 1 (EC 1.-.-.-) (AFB1-AR 1) (ALDOKETOREDUCTASE 7). [Source:SWISSPROT;Acc:O43488]	0.0621197	0.242271	0.256405843	AKR7A2	
946	VOLTAGE-GATED POTASSIUM CHANNEL BETA-2 SUBUNIT (K+ CHANNEL BETA-2 SUBUNIT) (KV-BETA-2) (HKVBETA2). [Source:SWISSPROT;Acc:Q13303]	0.0586077	0.228574	0.256405803	KCNAB2	
947	GOLGI MEMBRANE PROTEIN SB140; SMOOTH MUSCLE CELL ASSOCIATED PROTEIN 5. [Source:RefSeq;Acc:NM_030799]	0.174649	0.681143	0.256405777	YIPF5	
948	RAB ACCEPTOR 1 (PRENYLATED); PRENYLATED RAB ACCEPTOR 1. [Source:RefSeq;Acc:NM_006423]	0.13204	0.514965	0.256405775	RABAC1	
949	"OLIGORIBONUCLEASE, MITOCHONDRIAL PRECURSOR (EC 3.1.-.-) (SMALL FRAGMENT NUCLEASE) (CGI-114). [Source:SWISSPROT;Acc:Q9Y3B8]"	0.0337699	0.131705	0.256405603	REXO2	
950	VOLTAGE-GATED POTASSIUM CHANNEL BETA-1 SUBUNIT (K+ CHANNEL BETA-1 SUBUNIT) (KV-BETA-1). [Source:SWISSPROT;Acc:Q14722]	0.0645342	0.251688	0.25640555	KCNAB1	
951	"10 KDA HEAT SHOCK PROTEIN, MITOCHONDRIAL (HSP10) (10 KDA CHAPERONIN) (CPN10). [Source:SWISSPROT;Acc:Q04984]"	0.0645342	0.251688	0.25640555	HSPE1	

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/