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 501 to 550 of 3206 in total

measured	Hugo	Rank	expected	final	description
0.0374428	SLC4A1AP	2876	0.198705	0.188434111	"SOLUTE CARRIER FAMILY 4 (ANION EXCHANGER), MEMBER 1, ADAPTOR PROTEIN; KIDNEY ANION EXCHANGER ADAPTOR PROTEIN; KANADAPTIN; LUNG CANCER ONCOGENE 3. [RefSeq;Acc:NM_018158]"
0.0374644	DEGS1	978	0.146714	0.25535668	SPHINGOLIPID DELTA 4 DESATURASE; MEMBRANE FATTY ACID (LIPID) DESATURASE; DIHYDROCERAMIDE DESATURASE. [RefSeq;Acc:NM_003676]
0.0374708	ISY1	450	0.135742	0.27604426
0.0375812	FABP4	292	0.12452	0.301808545	"FATTY ACID-BINDING PROTEIN, ADIPOCYTE (AFABP) (ADIPOCYTE LIPID-BINDING PROTEIN) (ALBP) (A-FABP). [SWISSPROT;Acc:P15090]"
0.0375954	FAM50B	1337	0.153273	0.245283905	DNA SEGMENT ON CHROMOSOME 6(UNIQUE) 2654 EXPRESSED SEQUENCE; DNA SEGMENT ON CHROMOSOME X (UNIQUE) 2654 EXPRESSED SEQUENCE. [RefSeq;Acc:NM_012135]
0.0376313	LRRC4	541	0.138821	0.271077863	NAG14 PROTEIN. [RefSeq;Acc:NM_022143]
0.037683	C21orf66	1558	0.156176	0.241285473	GC-RICH SEQUENCE DNA-BINDING FACTOR HOMOLOG. [SWISSPROT;Acc:Q9Y5B6]
0.037683	TLR2	1559	0.156176	0.241285473	TOLL-LIKE RECEPTOR 2 PRECURSOR (TOLL/INTERLEUKIN 1 RECEPTOR-LIKE PROTEIN 4). [SWISSPROT;Acc:O60603]
0.0376832	BRF1	257	0.121057	0.311284767	"TRANSCRIPTION FACTOR IIIB 90 KDA SUBUNIT (TFIIIB90) (HTFIIIB90) (B- RELATED FACTOR 1) (HBRF) (TATA BOX-BINDING PROTEIN-ASSOCIATED FACTOR, RNA POLYMERASE III, SUBUNIT 2) (TAF3B2). [SWISSPROT;Acc:Q92994]"
0.0376993	FLNB	179	0.111754	0.33734184	"FILAMIN B, BETA (ACTIN BINDING PROTEIN 278); BETA FILAMIN; FILAMIN 1 (ACTIN-BINDING PROTEIN-280)-LIKE; FILAMIN B, BETA (ACTIN-BINDING PROTEIN-278); FILAMIN B, BETA. [RefSeq;Acc:NM_001457]"
0.0377474	TMCC2	792	0.144067	0.262012813
0.0377549	FAP	2540	0.175918	0.214616469	SEPRASE (EC 3.4.21.-) (FIBROBLAST ACTIVATION PROTEIN ALPHA) (INTEGRAL MEMBRANE SERINE PROTEASE) (170-KDA MELANOMA MEMBRANE-BOUND GELATINASE). [SWISSPROT;Acc:Q12884]
0.037776	no value	1386	0.154523	0.244468461	BA271B5.1 (SIMILAR TO RIBOSOMAL PROTEIN S7). [SPTREMBL;Acc:Q9H1S9]
0.0377969	SLC23A2	482	0.137792	0.274304023	"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). [SWISSPROT;Acc:Q9UGH3]"
0.0378274	no value	924	0.1468	0.257679837	FATTY ACID DESATURASE 1; LINOLEOYL-COA DESATURASE (DELTA-6-DESATURASE)-LIKE 1; DELTA-5 DESATURASE; DELTA-5 FATTY ACID DESATURASE. [RefSeq;Acc:NM_013402]
0.0378287	FUT8	991	0.148317	0.255053028	"ALPHA-(1,6)-FUCOSYLTRANSFERASE (EC 2.4.1.68) (GLYCOPROTEIN 6-ALPHA-L- FUCOSYLTRANSFERASE) (GDP-FUCOSE--GLYCOPROTEIN FUCOSYLTRANSFERASE) (GDP-L-FUC:N-ACETYL-BETA-D-GLUCOSAMINIDE ALPHA1,6-FUCOSYLTRANSFERASE) (ALPHA1-6FUCT) (FUCOSYLTRANSFERASE 8). [SW"
0.0378408	SLC20A2	2363	0.171772	0.220296672	"SOLUTE CARRIER FAMILY 20 (PHOSPHATE TRANSPORTER), MEMBER 2; GLVR-2; PIT-2; GIBBON APE LEUKEMIA VIRUS RECEPTOR 2; MURINE LEUKEMIA VIRUS, AMPHOTROPIC; RECEPTOR. [RefSeq;Acc:NM_006749]"
0.0378601	no value	784	0.144194	0.26256363
0.0378747	PGGT1B	926	0.146984	0.257679067	GERANYLGERANYL TRANSFERASE TYPE I BETA SUBUNIT (EC 2.5.1.-) (TYPE I PROTEIN GERANYL-GERANYLTRANSFERASE BETA SUBUNIT) (GGTASE-I-BETA). [SWISSPROT;Acc:P53609]
0.0378858	SHC3	476	0.138116	0.274304208	NEURONAL SHC. [RefSeq;Acc:NM_016848]
0.0379081	SHC2	475	0.138197	0.274304797	PROTEIN SCK (FRAGMENT). [SWISSPROT;Acc:P98077]
0.0379775	BCAS2	519	0.139495	0.272249901	"BREAST CARCINOMA AMPLIFIED SEQUENCE 2; SPLICEOSOME ASSOCIATED PROTEIN, AMPLIFIED IN BREAST CANCER. [RefSeq;Acc:NM_005872]"
0.0379885	GATAD2A	2901	0.217449	0.174700734	P66 ALPHA. [RefSeq;Acc:NM_017660]
0.0380979	OXR1	557	0.140583	0.270999338	OXIDATION RESISTANCE 1. [RefSeq;Acc:NM_181354]
0.0381158	WDR22	1110	0.151938	0.250864168
0.0382183	RPL34	1956	0.165264	0.231256051	60S RIBOSOMAL PROTEIN L34. [SWISSPROT;Acc:P49207]
0.0382473	PRMT8	175	0.113378	0.337343224	PROTEIN ARGININE N-METHYLTRANSFERASE 4 (EC 2.1.1.-). [SWISSPROT;Acc:Q9NR22]
0.0382656	no value	2526	0.178175	0.214764136	KERATIN ASSOCIATED PROTEIN 4-14; KERATIN ASSOCIATED PROTEIN 4.14. [RefSeq;Acc:NM_033059]
0.03829	EXO1	1076	0.151786	0.252263055	"EXONUCLEASE 1 ISOFORM B; RAD2 NUCLEASE FAMILY MEMBER, HOMOLOG OF S. CEREVISIAE EXONUCLEASE 1. [RefSeq;Acc:NM_006027]"
0.038293	RPS7	1388	0.156638	0.244468137	40S RIBOSOMAL PROTEIN S7 (S8). [SWISSPROT;Acc:P23821]
0.0383264	no value	2525	0.178458	0.214764258	KERATIN ASSOCIATED PROTEIN 4.9 (FRAGMENT). [SPTREMBL;Acc:Q9BYQ8]
0.038359	no value	1823	0.163741	0.234266311
	ANK2	1824			"ANKYRIN 2 (BRAIN ANKYRIN) (ANKYRIN B) (ANKYRIN, NONERYTHROID). [SWISSPROT;Acc:Q01484]"
	ARL3	1822			ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 3. [SWISSPROT;Acc:P36405]
0.0383868	EXOC3	1509	0.158229	0.24260281	EXOCYST COMPLEX COMPONENT SEC6. [SWISSPROT;Acc:O60645]
0.0384193	C8orf79	418	0.138512	0.277371636
0.038432	WDR82	1392	0.157255	0.244392865
0.0384502	MAEA	1616	0.160453	0.239635283
0.0384502	RMND5A	1617	0.160453	0.239635283
0.0384625	no value	1273	0.155989	0.246571874	KAPPA B-RAS 1. [RefSeq;Acc:NM_020345]
0.0384625	SNAPAP	1274	0.155989	0.246571874	SNARE ASSOCIATED PROTEIN SNAPIN. [RefSeq;Acc:NM_012437]
0.0385127	FAT	825	0.147402	0.261276645	CADHERIN-RELATED TUMOR SUPPRESSOR HOMOLOG PRECURSOR (FAT PROTEIN HOMOLOG). [SWISSPROT;Acc:Q14517]
	STARD3	824			MLN 64 PROTEIN (STAR-RELATED LIPID TRANSFER PROTEIN 3) (STARD3) (START DOMAIN-CONTAINING PROTEIN 3) (CAB1 PROTEIN). [SWISSPROT;Acc:Q14849]
	TANC1	823
0.0385424	LATS2	553	0.142223	0.270999768	"LATS, LARGE TUMOR SUPPRESSOR, HOMOLOG 2; LATS (LARGE TUMOR SUPPRESSOR, DROSOPHILA) HOMOLOG 2. [RefSeq;Acc:NM_014572]"
0.0385572	FABP7	282	0.127753	0.301810525	"FATTY ACID-BINDING PROTEIN, BRAIN (B-FABP) (BRAIN LIPID-BINDING PROTEIN) (BLBP) (MAMMARY DERIVED GROWTH INHIBITOR RELATED). [SWISSPROT;Acc:O15540]"
0.0385624	GTDC1	1119	0.153758	0.250799308
0.0385664	C16orf70	1578	0.160098	0.240892453	UPF0183 PROTEIN. [SWISSPROT;Acc:Q9BSU1]
0.0385694	BBS7	742	0.145821	0.264498255	BARDET-BIEDL SYNDROME 7 PROTEIN ISOFORM A; BBS2-LIKE 1. [RefSeq;Acc:NM_176824]
0.0385694	HSDL2	743	0.145821	0.264498255

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/