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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measured Hugo Gene Rank expected final description

Results: HTML CSV LaTeX

Showing element 252 to 301 of 3206 in total

measured	Hugo	Rank	expected	final	description
0.029	RRAGC	3201	1.21378	0.023892303	RAS-RELATED GTP BINDING C; RAG C PROTEIN. [RefSeq;Acc:NM_022157]
0.0290537	COQ10B	2054	0.126477	0.229715284
0.0291377	KIAA1033	2241	0.130208	0.223778109
0.0292681	DDX43	2972	0.208597	0.140309305	DEAD-BOX PROTEIN. [RefSeq;Acc:NM_018665]
0.0292681	TBCC	2971	0.208597	0.140309305	TUBULIN-SPECIFIC CHAPERONE C (TUBULIN-FOLDING COFACTOR C) (CFC). [SWISSPROT;Acc:Q15814]
0.0293247	GNG11	3050	0.274937	0.106659707	GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(O) GAMMA-11 SUBUNIT. [SWISSPROT;Acc:P50152]
0.0294363	HDGFL1	2871	0.155797	0.188940095	PWWP DOMAIN CONTAINING 1; HDGF (HEPATOMA-DERIVED GROWTH FACTOR) LIKE. [RefSeq;Acc:NM_138574]
0.0295551	GATAD2B	2900	0.169175	0.174701345	TRANSCRIPTION REPRESSOR P66 BETA COMPONENT OF THE MECP1 COMPLEX. [RefSeq;Acc:NM_020699]
0.0295892	C1orf50	2336	0.133775	0.22118632
0.029603	no value	2002	0.128294	0.230743449
0.0296502	no value	745	0.1121	0.26449777	BA508N22.1 (HSPC025) (FRAGMENT). [SPTREMBL;Acc:Q9HCW5]
0.0296703	MYL6	818	0.113537	0.261327144	"MYOSIN LIGHT CHAIN 1, SLOW-TWITCH MUSCLE A ISOFORM (MLC1SA) (ALKALI). [SWISSPROT;Acc:P14649]"
0.0296703	NDUFS6	817	0.113537	0.261327144	"NADH-UBIQUINONE OXIDOREDUCTASE 13 KDA-A SUBUNIT, MITOCHONDRIAL PRECURSOR (EC 1.6.5.3) (EC 1.6.99.3) (COMPLEX I-13KD-A) (CI-13KD-A). [SWISSPROT;Acc:O75380]"
0.0296714	ARL4A	1549	0.122715	0.241791142	ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 4. [SWISSPROT;Acc:P40617]
0.0297305	LTA4H	2268	0.133476	0.222740418	LEUKOTRIENE A-4 HYDROLASE (EC 3.3.2.6) (LTA-4 HYDROLASE) (LEUKOTRIENE A(4) HYDROLASE). [SWISSPROT;Acc:P09960]
0.0297584	TXN	1321	0.121182	0.245567824	THIOREDOXIN (ATL-DERIVED FACTOR) (ADF) (SURFACE ASSOCIATED SULPHYDRYL PROTEIN) (SASP). [SWISSPROT;Acc:P10599]
0.0298281	no value	827	0.114163	0.261276421	PUTATIVE ANKYRIN-REPEAT CONTAINING PROTEIN. [RefSeq;Acc:NM_025185]
0.0298356	DPY19L2	2112	0.130757	0.228175929
0.0298377	MAF1	2416	0.136653	0.218346469	HOMOLOG OF YEAST MAF1. [RefSeq;Acc:NM_032272]
0.0298377	SERINC3	2415	0.136653	0.218346469	TUMOR DIFFERENTIALLY EXPRESSED PROTEIN 1 (TRANSMEMBRANE PROTEIN SBBI99). [SWISSPROT;Acc:Q13530]
0.0299559	DDX39	1758	0.126548	0.236715713	"DEAD (ASP-GLU-ALA-ASP) BOX POLYPEPTIDE 39 ISOFORM 1; NUCLEAR RNA HELICASE, DECD VARIANT OF DEAD BOX FAMILY. [RefSeq;Acc:NM_005804]"
0.0299629	STARD3NL	828	0.114679	0.261276258	MLN64 N-TERMINAL DOMAIN HOMOLOG (STARD3 N-TERMINAL LIKE PROTEIN). [SWISSPROT;Acc:O95772]
0.0299967	ANK3	1818	0.128045	0.234266859	ANKYRIN 3 (ANK-3) (ANKYRIN G). [SWISSPROT;Acc:Q12955]
0.0300014	FAT2	822	0.114826	0.261277063	PROTOCADHERIN FAT 2 PRECURSOR (HFAT2) (MULTIPLE EPIDERMAL GROWTH FACTOR-LIKE DOMAINS 1). [SWISSPROT;Acc:Q9NYQ8]
0.0302145	CPXM1	1115	0.120464	0.250817672	POTENTIAL CARBOXYPEPTIDASE X PRECURSOR (EC 3.4.17.-) (METALLOCARBOXYPEPTIDASE CPX-1). [SWISSPROT;Acc:Q96SM3]
0.0302145	CPXM2	1114	0.120464	0.250817672	POTENTIAL CARBOXYPEPTIDASE-LIKE PROTEIN X2 PRECURSOR. [SWISSPROT;Acc:Q8N436]
0.0303013	GTF2F1	1715	0.127662	0.237355674	"TRANSCRIPTION INITIATION FACTOR IIF, ALPHA SUBUNIT (TFIIF-ALPHA) (TRANSCRIPTION INITIATION FACTOR RAP74). [SWISSPROT;Acc:P35269]"
0.0303497	KHK	830	0.116238	0.26109964	KETOHEXOKINASE (EC 2.7.1.3) (HEPATIC FRUCTOKINASE). [SWISSPROT;Acc:P50053]
0.0303657	ATP5S	1795	0.129305	0.234837787	"ATP SYNTHASE COUPLING FACTOR B, MITOCHONDRIAL PRECURSOR. [SWISSPROT;Acc:Q99766]"
0.0303816	CPZ	1111	0.12113	0.250818129	CPZ GENE PRODUCT. [RefSeq;Acc:NM_003652]
0.0303893	TBL1Y	1421	0.1246	0.243894864	"TRANSDUCIN BETA-LIKE 1Y PROTEIN (TRANSDUCIN-BETA-LIKE 1, Y-LINKED). [SWISSPROT;Acc:Q9BQ87]"
0.0303966	COQ3	1793	0.129436	0.234838839	"HEXAPRENYLDIHYDROXYBENZOATE METHYLTRANSFERASE, MITOCHONDRIAL PRECURSOR (EC 2.1.1.114) (DIHYDROXYHEXAPRENYLBENZOATE METHYLTRANSFERASE) (3,4- DIHYDROXY-5-HEXAPRENYLBENZOATE METHYLTRANSFERASE) (DHHB METHYLTRANSFERASE) (DHHB-MT) (DHHB-MTASE). [SWISSPRO"
0.0305282	TMCC1	808	0.116515	0.2620109
0.0305539	UXT	1788	0.129981	0.235064356	UXT PROTEIN (UBIQUITOUSLY EXPRESSED TRANSCRIPT PROTEIN) (HSPC024). [SWISSPROT;Acc:Q9UBK9]
0.0305539	VBP1	1787	0.129981	0.235064356	PREFOLDIN SUBUNIT 3 (VON HIPPEL-LINDAU BINDING PROTEIN 1) (VHL BINDING PROTEIN-1) (VBP-1) (HIBBJ46). [SWISSPROT;Acc:Q15765]
0.0305909	DAGLB	1974	0.13236	0.231118918	KCCR13L. [RefSeq;Acc:NM_139179]
0.0305968	ATP13A2	1189	0.123075	0.248602884	PROBABLE CATION-TRANSPORTING ATPASE 1 (EC 3.6.1.-). [SWISSPROT;Acc:Q9NQ11]
0.0305978	CPN1	1112	0.121992	0.250818086	CARBOXYPEPTIDASE N CATALYTIC CHAIN PRECURSOR (EC 3.4.17.3) (ARGININE CARBOXYPEPTIDASE) (KININASE 1) (SERUM CARBOXYPEPTIDASE N) (SCPN) (ANAPHYLATOXIN INACTIVATOR) (PLASMA CARBOXYPEPTIDASE B). [SWISSPROT;Acc:P15169]
0.0306345	TBL1X	1420	0.125605	0.243895546	"TRANSDUCIN BETA-LIKE 1X PROTEIN (TRANSDUCIN-BETA-LIKE 1, X-LINKED). [SWISSPROT;Acc:O60907]"
0.0306863	GTF2H1	3035	0.267389	0.114762761	TFIIH BASAL TRANSCRIPTION FACTOR COMPLEX P62 SUBUNIT (BASIC TRANSCRIPTION FACTOR 62 KDA SUBUNIT) (BTF2-P62) (GENERAL TRANSCRIPTION FACTOR IIH POLYPEPTIDE 1). [SWISSPROT;Acc:P32780]
0.0307397	APOB	1387	0.125741	0.244468391	APOLIPOPROTEIN B-100 PRECURSOR (APO B-100) [CONTAINS: APOLIPOPROTEIN B-48 (APO B-48)]. [SWISSPROT;Acc:P04114]
0.0307477	ORAI1	2860	0.162737	0.188941052
0.0307532	ARHGEF9	2089	0.13446	0.228716347	CDC42 GUANINE EXCHANGE FACTOR 9; HPEM-2 COLLYBISTIN. [RefSeq;Acc:NM_015185]
0.0308129	ITM2B	2407	0.140868	0.21873598	INTEGRAL MEMBRANE PROTEIN 2B (TRANSMEMBRANE PROTEIN BRI) [CONTAINS: ABRI/ADAN AMYLOID PEPTIDE]. [SWISSPROT;Acc:Q9Y287]
0.030826	PGAM4	1097	0.122661	0.251310522	PUTATIVE PHOSPHOGLYCERATE MUTASE 3 (EC 5.4.2.1) (EC 5.4.2.4) (EC 3.1.3.13). [SWISSPROT;Acc:Q8N0Y7]
0.030828500000000002	no value	2413	0.141189	0.218349163
0.0308447	no value	1481	0.126946	0.242974966
0.03085	ORAI2	2867	0.163279	0.188940403
0.0308655	no value	2978	0.221164	0.139559332	HOMEOBOX PROTEIN HOX-C6 (HOX-3C) (HHO.C8) (CP25). [SWISSPROT;Acc:P09630]
0.0308872	PSIP1	2869	0.163476	0.188940273	PC4 AND SFRS1 INTERACTING PROTEIN 2; PC4 AND SFRS1 INTERACTING PROTEIN 1; TRANSCRIPTIONAL COACTIVATOR P52/P75. [RefSeq;Acc:NM_033222]

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Hugo is the bloody hugo identifier as demanded by the BMC Bioinformatics idiots

- http://analysis.yellowcouch.org/