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 Hugo expected final

Results: HTML CSV LaTeX

Showing element 1 to 50 of 3206 in total

Rank	description	measured	Hugo	expected	final	
1	PROTEIN CGI-126 (PROTEIN HSPC155). [Source:SWISSPROT;Acc:Q9Y3C8]	0.790808	UFC1	0.682179	1.159238264	
2	RAD50-INTERACTING PROTEIN 1. [Source:RefSeq;Acc:NM_021930]	1.28125	RINT1	1.1674	1.097524413	
3	RHO-RELATED BTB DOMAIN-CONTAINING PROTEIN 2 (DELETED IN BREAST CANCER 2 GENE PROTEIN) (P83). [Source:SWISSPROT;Acc:Q9BYZ6]	1.28125	RHOBTB2	1.1674	1.097524413	
4		3.66001		3.3348	1.097520091	
5	"NADH-UBIQUINONE OXIDOREDUCTASE 18 KDA SUBUNIT, MITOCHONDRIAL PRECURSOR (EC 1.6.5.3) (EC 1.6.99.3) (COMPLEX I-18 KDA) (CI-18 KDA) (COMPLEX I- AQDQ) (CI-AQDQ). [Source:SWISSPROT;Acc:O43181]"	0.489705	NDUFS4	0.74385	0.658338375	
6	CHROMATIN ACCESSIBILITY COMPLEX PROTEIN 1 (CHRAC-1) (CHRAC-15) (HUCHRAC15) (DNA POLYMERASE EPSILON SUBUNIT P15). [Source:SWISSPROT;Acc:Q9NRG0]	0.590586	CHRAC1	0.969328	0.609273641	
7	ADIPONECTIN RECEPTOR 2. [Source:RefSeq;Acc:NM_024551]	0.252763	ADIPOR2	0.428531	0.589835975	
8	ODD-SKIPPED RELATED 1; ODZ (ODD OZ/TEN-M) RELATED 1. [Source:RefSeq;Acc:NM_145260]	0.281519	OSR1	0.487701	0.577236873	
9	DNA POLYMERASE EPSILON P12 SUBUNIT (DNA POLYMERASE EPSILON SUBUNIT 4). [Source:SWISSPROT;Acc:Q9NR33]	0.803534	POLE4	1.40271	0.572843995	
10	PROTEIN X 0004. [Source:RefSeq;Acc:NM_016301]	0.271296	ATPBD1C	0.5	0.542592	
11	XPA BINDING PROTEIN 1; MBD2 INTERACTOR PROTEIN; PUTATIVE ATP(GTP)-BINDING PROTEIN. [Source:RefSeq;Acc:NM_007266]	0.813888	XAB1	1.5	0.542592	
12	HBS1-LIKE. [Source:RefSeq;Acc:NM_006620]	0.250879	HBS1L	0.5	0.501758	
13	HOMEOBOX PROTEIN HLX1 (HOMEOBOX PROTEIN HB24). [Source:SWISSPROT;Acc:Q14774]	0.250879	HLX	0.5	0.501758	
14	NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT BETA (NF-Y PROTEIN CHAIN B) (NF-YB) (CCAAT-BINDING TRANSCRIPTION FACTOR SUBUNIT A) (CBF-A) (CAAT- BOX DNA BINDING PROTEIN SUBUNIT B). [Source:SWISSPROT;Acc:P25208]	0.439158	NFYB	0.912166	0.481445263	
15	GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2 (GRB2 ADAPTER PROTEIN) (SH2/SH3 ADAPTER GRB2) (ASH PROTEIN). [Source:SWISSPROT;Acc:P29354]	1.95189	GRB2	4.10415	0.475589342	
16	SERINE/THREONINE-PROTEIN KINASE NEK2 (EC 2.7.1.37) (NIMA-RELATED PROTEIN KINASE 2) (NIMA-LIKE PROTEIN KINASE 1) (HSPK 21). [Source:SWISSPROT;Acc:P51955]	0.106175	NEK2	0.22325	0.475587906	
17		0.0856348		0.180231	0.475139127	
18		0.0773877	FAM49B	0.162874	0.475138451	
19	E2A-PBX1-ASSOCIATED PROTEIN; PUTATIVE 47 KDA PROTEIN. [Source:RefSeq;Acc:NM_020140]	0.310118	ANKS1B	0.652691	0.475137546	
20	NEURON NAVIGATOR 1; NEURON NAVIGATOR-1; PORE MEMBRANE AND/OR FILAMENT INTERACTING LIKE PROTEIN 3. [Source:RefSeq;Acc:NM_020443]	0.149206	NAV1	0.314027	0.475137488	
21	NEURON NAVIGATOR 3; PORE MEMBRANE AND/OR FILAMENT INTERACTING LIKE PROTEIN 1; STEERIN 3. [Source:RefSeq;Acc:NM_014903]	0.150125	NAV3	0.315963	0.475134747	
22	NEURON NAVIGATOR 2 ISOFORM L; RETINOIC ACID INDUCIBLE IN NEUROBLASTOMA; PORE MEMBRANE AND/OR FILAMENT INTERACTING LIKE PROTEIN 2; HELICASE HELAD1. [Source:RefSeq;Acc:NM_145117]	0.192159	NAV2	0.404444	0.475118929	
23	GRB2-RELATED ADAPTOR PROTEIN. [Source:SWISSPROT;Acc:Q13588]	1.4649	GRAP	3.08715	0.47451533	
24		0.229891	CNOT10	0.5	0.459782	
25	DNA-REPAIR PROTEIN COMPLEMENTING XP-G CELLS (XERODERMA PIGMENTOSUM GROUP G COMPLEMENTING PROTEIN) (DNA EXCISION REPAIR PROTEIN ERCC-5). [Source:SWISSPROT;Acc:P28715]	0.364125	ERCC5	0.853699	0.426526211	
26	DOCKING PROTEIN 2 (P56(DOK-2)) (DOWNSTREAM OF TYROSINE KINASE 2). [Source:SWISSPROT;Acc:O60496]	0.0954445	DOK2	0.223986	0.42611815	
27	TYROSINE-PROTEIN KINASE FRK (EC 2.7.1.112) (NUCLEAR TYROSINE PROTEIN KINASE RAK). [Source:SWISSPROT;Acc:P42685]	0.643425	FRK	1.50997	0.426117737	
28	DOK-LIKE PROTEIN. [Source:RefSeq;Acc:NM_024872]	0.0753031		0.176719	0.426117735	
29	DOCKING PROTEIN 1 (P62(DOK)) (DOWNSTREAM OF TYROSINE KINASE 1) (PP62). [Source:SWISSPROT;Acc:Q99704]	0.0754466	DOK1	0.177056	0.426117161	
30	TATA-BINDING PROTEIN-ASSOCIATED PHOSPHOPROTEIN (DOWN-REGULATOR OF TRANSCRIPTION 1) (DR1 PROTEIN). [Source:SWISSPROT;Acc:Q01658]	0.263027	DR1	0.621928	0.422921946	
31	WISKOTT-ALDRICH SYNDROME PROTEIN (WASP). [Source:SWISSPROT;Acc:P42768]	1.97356	WAS	4.68345	0.421390214	
32	PROTO-ONCOGENE TYROSINE-PROTEIN KINASE SRC (EC 2.7.1.112) (P60-SRC) (C-SRC). [Source:SWISSPROT;Acc:P12931]	0.141847		0.33698	0.420935961	
33	TYROSINE-PROTEIN KINASE HCK (EC 2.7.1.112) (P59-HCK/P60-HCK) (HEMOPOIETIC CELL KINASE). [Source:SWISSPROT;Acc:P08631]	0.141847	HCK	0.33698	0.420935961	
34	PROTO-ONCOGENE C-CRK (P38) (ADAPTER MOLECULE CRK). [Source:SWISSPROT;Acc:P46108]	0.142264	CRK	0.337971	0.420935524	
35	CRK-LIKE PROTEIN. [Source:SWISSPROT;Acc:P46109]	0.142003	CRKL	0.337351	0.420935465	
36	PROTO-ONCOGENE TYROSINE-PROTEIN KINASE ABL1 (EC 2.7.1.112) (P150) (C-ABL). [Source:SWISSPROT;Acc:P00519]	0.143775	ABL1	0.341561	0.42093506	
37	PROTO-ONCOGENE TYROSINE-PROTEIN KINASE FGR (EC 2.7.1.112) (P55-FGR) (C-FGR). [Source:SWISSPROT;Acc:P09769]	0.14242	FGR	0.338342	0.42093503	
38	TYROSINE-PROTEIN KINASE ABL2 (EC 2.7.1.112) (TYROSINE KINASE ARG). [Source:SWISSPROT;Acc:P42684]	0.143514	ABL2	0.340942	0.420933766	
39	PROTO-ONCOGENE TYROSINE-PROTEIN KINASE FYN (EC 2.7.1.112) (P59-FYN) (SYN) (SLK). [Source:SWISSPROT;Acc:P06241]	0.14268	FYN	0.338961	0.420933382	
40	GRB2-RELATED ADAPTOR PROTEIN 2 (GADS PROTEIN) (GROWTH FACTOR RECEPTOR BINDING PROTEIN) (GRBLG) (GRF40 ADAPTOR PROTEIN) (GRF-40) (GRB-2-LIKE PROTEIN) (GRB2L) (GRBX) (P38) (HEMATOPOIETIC CELL-ASSOCIATED ADAPTOR PROTEIN GRPL) (ADAPTER PROTEIN GRID) (SH3-SH2-	0.160294	GRAP2	0.380812	0.420926862	
41	CCAAT DISPLACEMENT PROTEIN (CDP) (CUT-LIKE 1). [Source:SWISSPROT;Acc:P39880]	0.187173	CUTL1	0.444789	0.420813015	
42	HOMEOBOX PROTEIN CUX-2 (CUT-LIKE 2) (FRAGMENT). [Source:SWISSPROT;Acc:O14529]	0.147881	CUTL2	0.35143	0.420797883	
43	NEURAL WISKOTT-ALDRICH SYNDROME PROTEIN (N-WASP). [Source:SWISSPROT;Acc:O00401]	1.66627	WASL	3.96399	0.420351716	
44	HEPATOCYTE NUCLEAR FACTOR 4-ALPHA (HNF-4-ALPHA) (TRANSCRIPTION FACTOR HNF-4) (TRANSCRIPTION FACTOR 14). [Source:SWISSPROT;Acc:P41235]	0.144656	HNF4A	0.346879	0.417021497	
45	GROWTH ARREST AND DNA-DAMAGE-INDUCIBLE PROTEIN GADD45 GAMMA (CYTOKINE RESPONSIVE PROTEIN CR6). [Source:SWISSPROT;Acc:O95257]	0.203633	GADD45G	0.488304	0.417020954	
46	HEPATOCYTE NUCLEAR FACTOR 4-GAMMA (HNF-4-GAMMA). [Source:SWISSPROT;Acc:Q14541]	0.117156	HNF4G	0.280936	0.417020247	
47	GROWTH ARREST AND DNA-DAMAGE-INDUCIBLE PROTEIN GADD45 BETA (NEGATIVE GROWTH-REGULATORY PROTEIN MYD118) (MYELOID DIFFERENTIATION PRIMARY RESPONSE PROTEIN MYD118). [Source:SWISSPROT;Acc:O75293]	0.173246	GADD45B	0.415438	0.417020109	
48	GROWTH ARREST AND DNA-DAMAGE-INDUCIBLE PROTEIN GADD45 ALPHA (DNA- DAMAGE INDUCIBLE TRANSCRIPT 1) (DDIT1). [Source:SWISSPROT;Acc:P24522]	0.174044	GADD45A	0.417352	0.417019686	
49	FERRITIN HEAVY CHAIN (FERRITIN H SUBUNIT). [Source:SWISSPROT;Acc:P02794]	0.788413	FTH1	1.91686	0.411304425	
50	FERRITIN LIGHT CHAIN (FERRITIN L SUBUNIT). [Source:SWISSPROT;Acc:P02792]	0.0515298	FTL	0.125329	0.411156237	

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/