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 451 to 500 of 3206 in total 
Rank	description	measured	expected	final	Hugo	
451	XPA-BINDING PROTEIN 2 (HCNP PROTEIN) (PP3898). [Source:SWISSPROT;Acc:Q9HCS7]	0.441621	1.59982	0.27604418	XAB2	
452	"PROTEIN-TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 1 (EC 3.1.3.48) (PROTEIN-TYROSINE PHOSPHATASE 1B) (PTP-1B). [Source:SWISSPROT;Acc:P18031]"	0.215243	0.779889	0.27599184		
453	"PROTEIN-TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 2 (EC 3.1.3.48) (T- CELL PROTEIN-TYROSINE PHOSPHATASE) (TCPTP). [Source:SWISSPROT;Acc:P17706]"	0.173881	0.6302	0.275913996	PTPN2	
454	TRANSDUCIN BETA-LIKE 2 PROTEIN (WS BETA-TRANSDUCIN REPEATS PROTEIN) (WS-BETATRP) (WILLIAMS-BEUREN SYNDROME CHROMOSOME REGION 13 PROTEIN). [Source:SWISSPROT;Acc:Q9Y4P3]	0.132041	0.478695	0.275835344	TBL2	
455	MITOCHONDRIAL GTP BINDING PROTEIN ISOFORM V. [Source:RefSeq;Acc:NM_032620]	0.270501	0.981155	0.275696501	GTPBP3	
456		0.0394844	0.143261	0.275611646	ZMAT2	
457	SQUAMOUS CELL CARCINOMA ANTIGEN RECOGNIZED BY T CELLS 1; U4/U6.U5 TRI-SNRNP-ASSOCIATED 110 KDA PROTEIN; IGE AUTOANTIGEN; SART1(259) PROTEIN; SART1(800) PROTEIN. [Source:RefSeq;Acc:NM_005146]	0.35534	1.28928	0.275611194	SART1	
458	ZASP PROTEIN (FRAGMENT). [Source:SPTREMBL;Acc:Q9Y4Z3]	2.49065	9.03714	0.275601573	LDB3	
459	COLLAGEN ALPHA 3(IV) CHAIN PRECURSOR (GOODPASTURE ANTIGEN). [Source:SWISSPROT;Acc:Q01955]	0.0421286	0.15287	0.275584484	COL4A3	
460	COLLAGEN ALPHA 5(IV) CHAIN PRECURSOR. [Source:SWISSPROT;Acc:P29400]	0.0637349	0.231274	0.27558177699999997		
461	TRANSCRIPTIONAL CO-ACTIVATOR WITH PDZ-BINDING MOTIF (TAZ). [Source:RefSeq;Acc:NM_015472]	0.0702636	0.254965	0.275581354	WWTR1	
462	9 KDA PROTEIN. [Source:SWISSPROT;Acc:P13994]	0.0869671	0.315578	0.275580364	CCDC130	
463	65 KDA YES-ASSOCIATED PROTEIN (YAP65). [Source:SWISSPROT;Acc:P46937]	0.0869671	0.315578	0.275580364	YAP1	
464	MITOCHONDRIAL RIBOSOMAL PROTEIN L24. [Source:RefSeq;Acc:NM_024540]	0.0869671	0.315578	0.275580364	MRPL24	
465	E1A BINDING PROTEIN P400; P400 SWI2/SNF2-RELATED PROTEIN; CAGH32 PROTEIN; TRINUCLEOTIDE REPEAT CONTAINING 12. [Source:RefSeq;Acc:NM_015409]	0.0869671	0.315578	0.275580364	EP400	
466	LIM PROTEIN (SIMILAR TO RAT PROTEIN KINASE C-BINDING ENIGMA); ENIGMA HOMOLOG. [Source:RefSeq;Acc:NM_006457]	1.83106	6.64504	0.275552894	PDLIM5	
467	"STERILE ALPHA AND TIR MOTIF CONTAINING 1; STERILE ALPHA AND HEAT/ARMADILLO MOTIF PROTEIN, ORTHOLOG OF DROSOPHILA. [Source:RefSeq;Acc:NM_015077]"	0.305359	1.11055	0.274961956	SARM1	
468	GTP-BINDING PROTEIN ERA HOMOLOG (HERA) (FRAGMENT). [Source:SWISSPROT;Acc:O75616]	0.0444465	0.161679	0.274905832	ERAL1	
469	"TRIMETHYLLYSINE DIOXYGENASE, MITOCHONDRIAL PRECURSOR (EC 1.14.11.8) (EPSILON-TRIMETHYLLYSINE 2-OXOGLUTARATE DIOXYGENASE) (TML-ALPHA- KETOGLUTARATE DIOXYGENASE) (TML HYDROXYLASE) (TML DIOXYGENASE) (TMLD). [Source:SWISSPROT;Acc:Q9NVH6]"	0.218407	0.794482	0.274904907	TMLHE	
470	"PALLIDIN; PALLID (MOUSE) HOMOLOG, PALLIDIN. [Source:RefSeq;Acc:NM_012388]"	0.153744	0.559309	0.274882042	PLDN	
471	"CLEAVAGE AND POLYADENYLATION SPECIFIC FACTOR 6, 68 KD SUBUNIT; PRE-MRNA CLEAVAGE FACTOR IM (68KD); CLEAVAGE AND POLYADENYLATION SPECIFIC FACTOR 6, 68KD SUBUNIT; PRE-MRNA CLEAVAGE FACTOR I, 68KD SUBUNIT. [Source:RefSeq;Acc:NM_007007]"	1.05805	3.85379	0.274547913	CPSF6	
472	COP9 CONSTITUTIVE PHOTOMORPHOGENIC HOMOLOG SUBUNIT 3; COP9 COMPLEX SUBUNIT 3; JAB1-CONTAINING SIGNALOSOME SUBUNIT 3. [Source:RefSeq;Acc:NM_003653]	0.105796	0.385361	0.274537382	COPS3	
473	HEPATOCYTE NUCLEAR FACTOR 3-GAMMA (HNF-3G) (FORKHEAD BOX PROTEIN A3) (FORK HEAD-RELATED PROTEIN FKH H3). [Source:SWISSPROT;Acc:P55318]	0.483455	1.76198	0.274381662	FOXA3	
474	SEVEN IN ABSENTIA HOMOLOG 2. [Source:RefSeq;Acc:NM_005067]	0.454535	1.65694	0.274321943	SIAH2	
475	PROTEIN SCK (FRAGMENT). [Source:SWISSPROT;Acc:P98077]	0.0379081	0.138197	0.274304797	SHC2	
476	NEURONAL SHC. [Source:RefSeq;Acc:NM_016848]	0.0378858	0.138116	0.274304208	SHC3	
477	OVARIAN CARCINOMA IMMUNOREACTIVE ANTIGEN. [Source:RefSeq;Acc:NM_017830]	0.126731	0.462009	0.27430418	OCIAD1	
478	"SOLUTE CARRIER FAMILY 23, MEMBER 1 (SODIUM-DEPENDENT VITAMIN C TRANSPORTER 1) (HSVCT1) (NA(+)/L-ASCORBIC ACID TRANSPORTER 1) (YOLK SAC PERMEASE-LIKE MOLECULE 3). [Source:SWISSPROT;Acc:Q9UHI7]"	0.0444669	0.162108	0.274304168	SLC23A1	
479	SHC TRANSFORMING PROTEIN. [Source:SWISSPROT;Acc:P29353]	0.0444669	0.162108	0.274304168	SHC1	
480	DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 7 (EC 2.7.1.-) (MAP KINASE KINASE 7) (MAPKK 7) (MAPK/ERK KINASE 7) (JNK ACTIVATING KINASE 2) (C-JUN N-TERMINAL KINASE KINASE 2) (JNK KINASE 2) (JNKK 2). [Source:SWISSPROT;Acc:O14733]	0.209195	0.762639	0.274304094	MAP2K7	
481	ADP-RIBOSYLATION FACTOR 3. [Source:SWISSPROT;Acc:P16587]	0.224714	0.819215	0.274304059	ARF3	
482	"SOLUTE CARRIER FAMILY 23, MEMBER 2 (SODIUM-DEPENDENT VITAMIN C TRANSPORTER 2) (HSVCT2) (NA(+)/L-ASCORBIC ACID TRANSPORTER 2) (YOLK SAC PERMEASE-LIKE MOLECULE 2) (NUCLEOBASE TRANSPORTER-LIKE 1 PROTEIN). [Source:SWISSPROT;Acc:Q9UGH3]"	0.0377969	0.137792	0.274304023	SLC23A2	
483	HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN A1 (HELIX-DESTABILIZING PROTEIN) (SINGLE-STRAND BINDING PROTEIN) (HNRNP CORE PROTEIN A1). [Source:SWISSPROT;Acc:P09651]	0.0703022	0.256293	0.274304019	HNRNPA1	
484	HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEINS A2/B1 (HNRNP A2 / HNRNP B1). [Source:SWISSPROT;Acc:P22626]	0.0539161	0.196556	0.274304015	HNRNPA2B1	
485		0.0257019	0.0936986	0.274303992	CHCHD3	
486	ADP-RIBOSYLATION FACTOR 1. [Source:SWISSPROT;Acc:P32889]	0.384939	1.40333	0.274303977	ARF1	
487	HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN A3 (HNRNP A3) (D10S102). [Source:SWISSPROT;Acc:P51991]	0.0562729	0.205148	0.274303917	HNRPA3	
488	ADP-RIBOSYLATION FACTOR 4. [Source:SWISSPROT;Acc:P18085]	0.106754	0.389182	0.274303539	ARF4	
489	"ZINC FINGER PROTEIN 289, ID1 REGULATED; LIKELY ORTHOLOG OF MOUSE ZFP289. [Source:RefSeq;Acc:NM_032389]"	0.02648	0.0965355	0.274303236	ZNF289	
490		0.0344618	0.125634	0.274303135	CHCHD6	
491	ADP-RIBOSYLATION FACTOR GTPASE-ACTIVATING PROTEIN 3 (ARF GAP 3). [Source:SWISSPROT;Acc:Q9NP61]	0.0344618	0.125634	0.274303135	ARFGAP3	
492		0.0344618	0.125634	0.274303135		
493	"POTASSIUM CHANNEL MODULATORY FACTOR 1; POTASSIUM CHANNEL MODULATORY FACTOR; DIFFERENTIALLY EXPRESSED IN BRANCHING TUBULOGENESIS 91; ZINC FINGER, ZZ DOMAIN CONTAINING 1. [Source:RefSeq;Acc:NM_020122]"	0.0341617	0.12454	0.274303035	KCMF1	
494	FUSED TOES HOMOLOG; LIKELY ORTHOLOG OF MOUSE FUSED TOES. [Source:RefSeq;Acc:NM_022476]	0.277907	1.01314	0.274302663	AKTIP	
495	R3H DOMAIN PROTEIN 1. [Source:SWISSPROT;Acc:Q15032]	0.309779	1.12934	0.274300919	R3HDM1	
496	MITOCHONDRIAL RIBOSOMAL PROTEIN L18. [Source:RefSeq;Acc:NM_014161]	0.0800469	0.291858	0.274266595	MRPL18	
497		0.25596	0.9333	0.274252652	R3HDM2	
498		0.236585	0.862726	0.274229593		
499	SEVEN IN ABSENTIA HOMOLOG 1. [Source:RefSeq;Acc:NM_003031]	0.563143	2.05361	0.274221006		
500	ABL-INTERACTOR 2; ABL-INTERACTING PROTEIN 1 (SH3-CONTAINING PROTEIN); ABL BINDING PROTEIN 3; ARG PROTEIN TYROSINE KINASE-BINDING PROTEIN; ABL-INTERACTOR PROTEIN 2B; SIMILAR TO SPECTRIN SH3 DOMAIN BINDING PROTEIN 1. [Source:RefSeq;Acc:NM_005759]	0.315262	1.14976	0.274198094	ABI2	

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/