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:
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Rank Gene description measured expected final Hugo
Results: HTML CSV LaTeX Showing element 51 to 100 of 3206 in total 
Rank	description	measured	expected	final	Hugo	
51	LIMKAIN B1. [Source:RefSeq;Acc:NM_019081]	0.0656049	0.159562	0.411156165	KIAA0430	
52	KININOGEN PRECURSOR (ALPHA-2-THIOL PROTEINASE INHIBITOR) [CONTAINS: BRADYKININ]. [Source:SWISSPROT;Acc:P01042]	0.586469	1.42639	0.411156135	KNG1	
53	DISKS LARGE-ASSOCIATED PROTEIN 2 (DAP-2) (SAP90/PSD-95-ASSOCIATED PROTEIN 2) (SAPAP2) (PSD-95/SAP90 BINDING PROTEIN 2) (FRAGMENT). [Source:SWISSPROT;Acc:Q9P1A6]	0.318849	0.775495	0.411155456		
54	PUTATIVE ADENOSYLHOMOCYSTEINASE 2 (EC 3.3.1.1) (S-ADENOSYL-L- HOMOCYSTEINE HYDROLASE) (ADOHCYASE). [Source:SWISSPROT;Acc:O43865]	0.25896	0.629835	0.411155303	AHCYL1	
55		0.231369	0.562729	0.411155281		
56	DISKS LARGE-ASSOCIATED PROTEIN 1 (DAP-1) (GUANYLATE KINASE-ASSOCIATED PROTEIN) (HGKAP) (SAP90/PSD-95-ASSOCIATED PROTEIN 1) (SAPAP1) (PSD- 95/SAP90 BINDING PROTEIN 1). [Source:SWISSPROT;Acc:O14490]	0.378587	0.920789	0.411154999	DLGAP1	
57	DISKS LARGE-ASSOCIATED PROTEIN 4 (DAP-4) (SAP90/PSD-95-ASSOCIATED PROTEIN 4) (SAPAP4) (PSD-95/SAP90 BINDING PROTEIN 4). [Source:SWISSPROT;Acc:Q9Y2H0]	0.378587	0.920789	0.411154999	DLGAP4	
58	"DJ681N20.2 (NOVEL PROTEIN SIMILAR TO FERRITIN, LIGHT POLYPEPTIDE (FTL)). [Source:SPTREMBL;Acc:Q9BYW6]"	0.0511645	0.124441	0.411154684		
59	DISKS LARGE-ASSOCIATED PROTEIN 3 (DAP-3) (SAP90/PSD-95-ASSOCIATED PROTEIN 3) (SAPAP3) (PSD-95/SAP90 BINDING PROTEIN 3) (FRAGMENT). [Source:SWISSPROT;Acc:O95886]	0.28264	0.68743	0.41115459	DLGAP3	
60	CELLULAR REPRESSOR OF E1A-STIMULATED GENES. [Source:RefSeq;Acc:NM_003851]	0.312681	0.760495	0.411154577	CREG1	
61	PUTATIVE ADENOSYLHOMOCYSTEINASE 3 (EC 3.3.1.1) (S-ADENOSYL-L- HOMOCYSTEINE HYDROLASE) (ADOHCYASE). [Source:SWISSPROT;Acc:Q96HN2]	0.312681	0.760495	0.411154577		
62	CELLULAR REPRESSOR OF E1A-STIMULATED GENES 2. [Source:RefSeq;Acc:NM_153836]	0.237385	0.577362	0.411154527	CREG2	
63	MITOCHONDRIAL FERRITIN; FERRITIN HEAVY CHAIN-LIKE; FERRITIN H SUBUNIT. [Source:RefSeq;Acc:NM_177478]	0.685868	1.66819	0.411145013	FTMT	
64	FERRITIN HEAVY POLYPEPTIDE-LIKE 17. [Source:SWISSPROT;Acc:Q9BXU8]	0.605547	1.4734	0.410986154	FTHL17	
65	DNA POLYMERASE EPSILON P17 SUBUNIT (DNA POLYMERASE EPSILON SUBUNIT 3) (CHROMATIN ACCESSIBILITY COMPLEX 17) (HUCHRAC17) (CHRAC-17). [Source:SWISSPROT;Acc:Q9NRF9]	0.446035	1.09489	0.407378823	POLE3	
66	SYNAPSIN I (BRAIN PROTEIN 4.1). [Source:SWISSPROT;Acc:P17600]	0.132875	0.327175	0.406128219	SYN1	
67	PEROXISOMAL TARGETING SIGNAL 1 RECEPTOR (PEROXISMORE RECEPTOR 1) (PEROXISOMAL C-TERMINAL TARGETING SIGNAL IMPORT RECEPTOR) (PTS1-BP) (PEROXIN-5) (PTS1 RECEPTOR). [Source:SWISSPROT;Acc:P50542]	1.42729	3.51439	0.406127379	PEX5	
68	HAIRY/ENHANCER-OF-SPLIT RELATED WITH YRPW MOTIF 1 (HAIRY AND ENHANCER OF SPLIT RELATED-1) (HESR-1) (CARDIOVASCULAR HELIX-LOOP-HELIX FACTOR 2) (HES-RELATED REPRESSOR PROTEIN 2 HERP2). [Source:SWISSPROT;Acc:Q9Y5J3]	0.0646859	0.159275	0.406127139	HEY1	
69	SYNAPSIN II. [Source:SWISSPROT;Acc:Q92777]	0.159227	0.392062	0.406127092	SYN2	
70	HAIRY/ENHANCER-OF-SPLIT RELATED WITH YRPW MOTIF-LIKE. [Source:RefSeq;Acc:NM_014571]	0.0617004	0.151924	0.406126748	HEYL	
71	ACTIN BINDING LIM PROTEIN 2. [Source:RefSeq;Acc:NM_032432]	0.0620387	0.152757	0.406126724	ABLIM2	
72	"DELTA3,5-DELTA2,4-DIENOYL-COA ISOMERASE, MITOCHONDRIAL PRECURSOR (EC 5.3.3.-). [Source:SWISSPROT;Acc:Q13011]"	0.31296	0.770597	0.406126678	ECH1	
73	TRANSCRIPTION FACTOR HES-1 (HAIRY AND ENHANCER OF SPLIT 1) (HAIRY- LIKE) (HHL) (HAIRY HOMOLOG). [Source:SWISSPROT;Acc:Q14469]	0.285613	0.703261	0.406126602	HES1	
74	HAIRY/ENHANCER-OF-SPLIT RELATED WITH YRPW MOTIF 2; GRIDLOCK; HES-RELATED REPRESSOR PROTEIN 1. [Source:RefSeq;Acc:NM_012259]	0.0796134	0.196031	0.406126582	HEY2	
75	MITOCHONDRIAL RIBOSOME RECYCLING FACTOR. [Source:RefSeq;Acc:NM_138777]	0.291345	0.717375	0.406126503	MRRF	
76		0.212647	0.523598	0.406126456	C22orf9	
77		0.0637106	0.156874	0.406125935	ABLIM3	
78	ASPARTATE BETA-HYDROXYLASE ISOFORM B; JUNCTIN ISOFORM 1; JUNCTATE; ASPARTYL/ASPARAGINYL-BETA-HYDROXYLASE; PEPTIDE-ASPARTATE BETA-DIOXYGENASE; HUMBUG. [Source:RefSeq;Acc:NM_032468]	0.06383	0.157168	0.406125929		
79	SYNAPSIN III. [Source:SWISSPROT;Acc:O14994]	0.133193	0.32796	0.406125747	SYN3	
80	ACTIN-BINDING LIM PROTEIN 1 ISOFORM A; LIM ACTIN-BINDING PROTEIN 1; LIMATIN; ACTIN-BINDING LIM PROTEIN. [Source:RefSeq;Acc:NM_002313]	0.0763094	0.187896	0.406125729	ABLIM1	
81	TRANSCRIPTION FACTOR DP-2 (E2F DIMERIZATION PARTNER 2). [Source:SWISSPROT;Acc:Q14188]	0.745698	1.87445	0.397822295	TFDP2	
82	TRANSCRIPTION FACTOR E2F1 (E2F-1) (RETINOBLASTOMA BINDING PROTEIN 3) (RBBP-3) (PRB-BINDING PROTEIN E2F-1) (PBR3) (RETINOBLASTOMA-ASSOCIATED PROTEIN 1) (RBAP-1). [Source:SWISSPROT;Acc:Q01094]	0.198685	0.505165	0.393307137	E2F1	
83	TRANSCRIPTION FACTOR E2F2 (E2F-2). [Source:SWISSPROT;Acc:Q14209]	0.204365	0.519607	0.393306865	E2F2	
84	EUKARYOTIC TRANSLATION INITIATION FACTOR 5 (EIF-5). [Source:SWISSPROT;Acc:P55010]	0.375556	0.956345	0.392699287	EIF5	
85	TRANSCRIPTION FACTOR DP-1 (E2F DIMERIZATION PARTNER 1) (DRTF1- POLYPEPTIDE-1) (DRTF1). [Source:SWISSPROT;Acc:Q14186]	0.788778	2.02915	0.388723357		
86	RGS19-INTERACTING PROTEIN 1 (GAIP C-TERMINUS INTERACTING PROTEIN GIPC) (RGS-GAIP INTERACTING PROTEIN) (TAX INTERACTION PROTEIN 2) (TIP-2). [Source:SWISSPROT;Acc:O14908]	1.20591	3.1266	0.385693725	GIPC1	
87		0.113929	0.295729	0.38524798	PLEKHG6	
88	APICAL-LIKE PROTEIN (APXL PROTEIN). [Source:SWISSPROT;Acc:Q13796]	0.117195	0.30421	0.385243746	SHROOM2	
89		0.152828	0.396725	0.385224022		
90	SHROOM-RELATED PROTEIN; F-ACTIN-BINDING PROTEIN; LIKELY ORTHOLOG OF MOUSE SHROOM. [Source:RefSeq;Acc:NM_020859]	0.152828	0.396725	0.385224022	SHROOM3	
91		0.152828	0.396725	0.385224022	SHROOM4	
92		0.914796	2.37847	0.38461532		
93	SIGNAL TRANSDUCTION PROTEIN CBL-B (SH3-BINDING PROTEIN CBL-B). [Source:SWISSPROT;Acc:Q13191]	0.502064	1.32571	0.378713293	CBLB	
94	CBL E3 UBIQUITIN PROTEIN LIGASE (EC 6.3.2.-) (SIGNAL TRANSDUCTION PROTEIN CBL) (PROTO-ONCOGENE C-CBL). [Source:SWISSPROT;Acc:P22681]	0.394562	1.04353	0.378103169	CBL	
95	POTASSIUM VOLTAGE-GATED CHANNEL SUBFAMILY A MEMBER 2 (POTASSIUM CHANNEL KV1.2) (RBK2) (HBK5) (NGK1) (MK2) (HUKIV). [Source:SWISSPROT;Acc:P16389]	0.22158	0.589242	0.376042441	KCNA2	
96	POTASSIUM VOLTAGE-GATED CHANNEL SUBFAMILY A MEMBER 1 (POTASSIUM CHANNEL KV1.1) (HUKI) (HBK1). [Source:SWISSPROT;Acc:Q09470]	0.185899	0.494524	0.375915021	KCNA1	
97	POTASSIUM VOLTAGE-GATED CHANNEL SUBFAMILY A MEMBER 4 (POTASSIUM CHANNEL KV1.4) (HK1) (HPCN2) (HBK4) (HUKII). [Source:SWISSPROT;Acc:P22459]	0.166283	0.442453	0.375820709	KCNA4	
98	VAV PROTO-ONCOGENE. [Source:SWISSPROT;Acc:P15498]	0.379284	1.01082	0.375224076	VAV1	
99	VAV-3 PROTEIN. [Source:SWISSPROT;Acc:Q9UKW4]	0.380273	1.015	0.374653202	VAV3	
100	"INOSITOL POLYPHOSPHATE-4-PHOSPHATASE, TYPE 1 ISOFORM B; INOSITOL POLYPHOSPHATE-4-PHOSPHATASE, TYPE I, 107KD; 4-PHOSPHATASE I; INOSITOL POLYPHOSPHATE-4-PHOSPHATASE I. [Source:RefSeq;Acc:NM_001566]"	0.0619579	0.165754	0.373794298	INPP4A	

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/