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 858 to 907 of 3206 in total 
Rank	description	measured	expected	final	Hugo	
858	SIGNAL TRANSDUCER AND ACTIVATOR OF TRANSCRIPTION 1-ALPHA/BETA (TRANSCRIPTION FACTOR ISGF-3 COMPONENTS P91/P84). [Source:SWISSPROT;Acc:P42224]	0.331884	1.2742	0.260464605	STAT1	
859	U4/U6 SMALL NUCLEAR RIBONUCLEOPROTEIN PRP4 (U4/U6 SNRNP 60 KDA PROTEIN) (WD SPLICING FACTOR PRP4) (HPRP4). [Source:SWISSPROT;Acc:O43172]	0.0530266	0.203611	0.26043092	PRPF4	
860	HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN K (HNRNP K) (DC-STRETCH BINDING PROTEIN) (CSBP) (TRANSFORMATION UPREGULATED NUCLEAR PROTEIN) (TUNP). [Source:SWISSPROT;Acc:Q07244]	0.35663	1.36939	0.260429826	HNRPK	
861	TWINKLE; LIKELY ORTHOLOG OF MOUSE T7 GP4-LIKE PROTEIN WITH INTRAMITOCHONDRIAL NUCLEOID LOCALIZATION. [Source:RefSeq;Acc:NM_021830]	0.176631	0.678587	0.260292343	PEO1	
862		0.0441578	0.169647	0.260292254	PYROXD1	
863	"RABAPTIN, RAB GTPASE BINDING EFFECTOR PROTEIN 1; RABAPTIN-5; NEUROCRESCIN. [Source:RefSeq;Acc:NM_004703]"	0.0441578	0.169647	0.260292254	RABEP1	
864	40S RIBOSOMAL PROTEIN S30. [Source:SWISSPROT;Acc:Q05472]	0.124733	0.479216	0.26028555	FAU	
865	"PRESYNAPTIC PROTEIN SAP97 (SYNAPSE-ASSOCIATED PROTEIN 97) (DISCS, LARGE HOMOLOG 1) (HDLG). [Source:SWISSPROT;Acc:Q12959]"	0.16564	0.636381	0.260284327	DLG1	
866	"CHANNEL ASSOCIATED PROTEIN OF SYNAPSE-110 (CHAPSYN-110) (DISCS, LARGE HOMOLOG 2). [Source:SWISSPROT;Acc:Q15700]"	0.141754	0.544635	0.260273394	DLG2	
867	"PRESYNAPTIC PROTEIN SAP102 (SYNAPSE-ASSOCIATED PROTEIN 102) (NEUROENDOCRINE-DLG) (NE-DLG) (DISCS, LARGE HOMOLOG 3). [Source:SWISSPROT;Acc:Q92796]"	0.138045	0.530387	0.260272216	DLG3	
868	"PRESYNAPTIC DENSITY PROTEIN 95 (PSD-95) (DISCS, LARGE HOMOLOG 4) (POSTSYNAPTIC DENSITY-95). [Source:SWISSPROT;Acc:P78352]"	0.138678	0.53282	0.260271762	DLG4	
869	HOMEOBOX PROTEIN BARH-LIKE 1. [Source:SWISSPROT;Acc:Q9HBU1]	0.139848	0.537326	0.260266579	BARX1	
870	T-CELL LEUKEMIA HOMEOBOX PROTEIN 2 (HOMEOBOX PROTEIN HOX-11L1) (NEURAL CREST HOMEOBOX PROTEIN). [Source:SWISSPROT;Acc:O43763]	0.0368198	0.14147	0.260265781	TLX2	
871	T-CELL LEUKEMIA HOMEOBOX PROTEIN 3 (HOMEOBOX PROTEIN HOX-11L2). [Source:SWISSPROT;Acc:O43711]	0.0457909	0.175939	0.260265774	TLX3	
872	OPSIN 4 (MELANOPSIN). [Source:SWISSPROT;Acc:Q9UHM6]	0.0585668	0.225027	0.260265657	OPN4	
873	T-CELL LEUKEMIA HOMEOBOX PROTEIN 1 (HOMEOBOX PROTEIN HOX-11) (TCL-3 PROTO-ONCOGENE). [Source:SWISSPROT;Acc:P31314]	0.0374306	0.143817	0.260265476	TLX1	
874	HECT DOMAIN CONTAINING PROTEIN 1 (FRAGMENT). [Source:SWISSPROT;Acc:Q9ULT8]	0.0211489	0.081259	0.260265324	HECTD1	
875	HOMEOBOX PROTEIN BARH-LIKE 2. [Source:SWISSPROT;Acc:Q9UMQ3]	0.109193	0.419545	0.260265287	BARX2	
876	U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM5. [Source:SWISSPROT;Acc:Q9Y4Y9]	0.196219	0.754024	0.260229117	LSM5	
877	T54 PROTEIN. [Source:SWISSPROT;Acc:Q92917]	0.314497	1.20911	0.260106194	GPKOW	
878	PUTATIVE PRE-MRNA SPLICING FACTOR RNA HELICASE (ATP-DEPENDENT RNA HELICASE #3) (DEAH-BOX PROTEIN 16). [Source:SWISSPROT;Acc:O60231]	0.039713	0.15268	0.260106104		
879		1.02292	3.93312	0.260078513	ARRDC2	
880	DYNAMIN 1-LIKE PROTEIN ISOFORM 3; DYNAMIN-LIKE PROTEIN. [Source:RefSeq;Acc:NM_005690]	0.121609	0.467587	0.260077804	DNM1L	
881	"PHOSPHOINOSITIDE-3-KINASE, CLASS 2, ALPHA POLYPEPTIDE; C2-CONTAINING PHOSPHATIDYLINOSITOL KINASE. [Source:RefSeq;Acc:NM_002645]"	0.0345092	0.132688	0.260077776	PIK3C2A	
882	PHOSPHATIDYLINOSITOL-4-PHOSPHATE 3-KINASE C2 DOMAIN-CONTAINING GAMMA POLYPEPTIDE (EC 2.7.1.154) (PHOSPHOINOSITIDE 3-KINASE-C2-GAMMA) (PTDINS-3-KINASE C2 GAMMA) (PI3K-C2GAMMA). [Source:SWISSPROT;Acc:O75747]	0.0242456	0.0932247	0.260076997	PIK3C2G	
883	PHOSPHATIDYLINOSITOL-4-PHOSPHATE 3-KINASE C2 DOMAIN-CONTAINING BETA POLYPEPTIDE (EC 2.7.1.154) (PHOSPHOINOSITIDE 3-KINASE-C2-BETA) (PTDINS-3-KINASE C2 BETA) (PI3K-C2BETA) (C2-PI3K). [Source:SWISSPROT;Acc:O00750]	0.0265832	0.102213	0.260076507	PIK3C2B	
884	SCRIBBLE. [Source:RefSeq;Acc:NM_015356]	0.163652	0.629348	0.260034194	SCRIB	
885	LAP (LEUCINE-RICH REPEATS AND PDZ) AND NO PDZ PROTEIN. [Source:RefSeq;Acc:NM_018214]	0.122677	0.471848	0.259992625	LRRC1	
886	KINESIN HEAVY CHAIN ISOFORM 5C (KINESIN HEAVY CHAIN NEURON-SPECIFIC 2). [Source:SWISSPROT;Acc:O60282]	0.152626	0.587298	0.25987829	KIF5C	
887	KINESIN LIGHT CHAIN 2 (KLC 2). [Source:SWISSPROT;Acc:Q9H0B6]	0.527178	2.02856	0.259877943	KLC2	
888	EXOCYST COMPLEX COMPONENT SEC3 (BM-012). [Source:SWISSPROT;Acc:Q9NV70]	0.0775579	0.29844	0.259877697	EXOC1	
889	NEURONAL KINESIN HEAVY CHAIN (NKHC) (KINESIN HEAVY CHAIN ISOFORM 5A) (KINESIN HEAVY CHAIN NEURON-SPECIFIC 1). [Source:SWISSPROT;Acc:Q12840]	0.131576	0.5063	0.259877543	KIF5A	
890	TRANSCRIPTION FACTOR IIIA (FACTOR A) (TFIIIA). [Source:SWISSPROT;Acc:Q92664]	0.0755679	0.290783	0.259877297	GTF3A	
891	RHO-GTPASE-ACTIVATING PROTEIN 8. [Source:SWISSPROT;Acc:Q9NSG0]	0.0962556	0.370389	0.259877048	PRR5	
892		0.0770577	0.296516	0.259877039	TMEM53	
893	RHO-GTPASE-ACTIVATING PROTEIN 1 (GTPASE-ACTIVATING PROTEIN RHOOGAP) (RHO-RELATED SMALL GTPASE PROTEIN ACTIVATOR) (CDC42 GTPASE-ACTIVATING PROTEIN) (P50-RHOGAP). [Source:SWISSPROT;Acc:Q07960]	0.119625	0.460314	0.259876954	ARHGAP1	
894	KINESIN HEAVY CHAIN (UBIQUITOUS KINESIN HEAVY CHAIN) (UKHC). [Source:SWISSPROT;Acc:P33176]	0.131086	0.504416	0.259876768	KIF5B	
895	KINESIN LIGHT CHAIN 1 (KLC 1). [Source:SWISSPROT;Acc:Q07866]	0.684483	2.63388	0.259876304	KLC1	
896		0.161768	0.623248	0.259556388	PRPF38B	
897	VACUOLAR PROTEIN SORTING 18 (HVPS18). [Source:SWISSPROT;Acc:Q9P253]	0.21331	0.821874	0.259541	VPS18	
898	WILMS' TUMOR 1-ASSOCIATING PROTEIN (WT1-ASSOCIATED PROTEIN). [Source:SWISSPROT;Acc:Q15007]	0.0746561	0.287738	0.259458605	WTAP	
899	SIGNAL RECOGNITION PARTICLE 68 KDA PROTEIN (SRP68). [Source:SWISSPROT;Acc:Q9UHB9]	0.193159	0.744637	0.259400218	SRP68	
900		0.0403612	0.155595	0.259399081	TEX9	
901	SPLICING FACTOR ARGININE/SERINE-RICH 11 (ARGININE-RICH 54 KDA NUCLEAR PROTEIN) (P54). [Source:SWISSPROT;Acc:Q05519]	0.148259	0.571608	0.259371807	SFRS11	
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	

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/