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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measured Hugo Gene Rank expected final description

Results: HTML CSV LaTeX

Showing element 401 to 450 of 3206 in total

measured	Hugo	Rank	expected	final	description
0.0337015	RPAP1	2461	0.155511	0.216714573
0.0337015	TADA3L	2463	0.155511	0.216714573	TRANSCRIPTIONAL ADAPTOR 3-LIKE ISOFORM A. [RefSeq;Acc:NM_006354]
0.0337208	NHP2L1	397	0.121119	0.278410489	NHP2-LIKE PROTEIN 1 (HIGH MOBILITY GROUP-LIKE NUCLEAR PROTEIN 2 HOMOLOG 1) ([U4/U6.U5] TRI-SNRNP 15.5 KDA PROTEIN) (OTK27). [SWISSPROT;Acc:P55769]
0.0337232	IGBP1	1599	0.140465	0.240082583	IMMUNOGLOBULIN-BINDING PROTEIN 1 (CD79A-BINDING PROTEIN 1) (B CELL SIGNAL TRANSDUCTION MOLECULE ALPHA 4) (ALPHA 4 PROTEIN). [SWISSPROT;Acc:P78318]
0.0337699	REXO2	949	0.131705	0.256405603	"OLIGORIBONUCLEASE, MITOCHONDRIAL PRECURSOR (EC 3.1.-.-) (SMALL FRAGMENT NUCLEASE) (CGI-114). [SWISSPROT;Acc:Q9Y3B8]"
0.0337842	ARFGEF1	1494	0.139157	0.242777582	BREFELDIN A-INHIBITED GUANINE NUCLEOTIDE-EXCHANGE PROTEIN 1 (BREFELDIN A-INHIBITED GEP 1) (P200 ARF-GEP1) (P200 ARF GUANINE NUCLEOTIDE EXCHANGE FACTOR). [SWISSPROT;Acc:Q9Y6D6]
0.0338352	FKBP1A	1519	0.13962	0.242337774	FK506-BINDING PROTEIN 1A (EC 5.2.1.8) (PEPTIDYL-PROLYL CIS-TRANS ISOMERASE) (PPIASE) (ROTAMASE) (12 KDA FKBP) (FKBP-12) (IMMUNOPHILIN FKBP12). [SWISSPROT;Acc:P20071]
0.0338352	SOCS1	1518	0.13962	0.242337774	SUPPRESSOR OF CYTOKINE SIGNALING 1 (SOCS-1) (JAK-BINDING PROTEIN) (JAB) (STAT INDUCED STAT INHIBITOR 1) (SSI-1) (TEC-INTERACTING PROTEIN 3) (TIP-3). [SWISSPROT;Acc:O15524]
0.0338955	ASNSD1	1699	0.142498	0.237866496	HCV NS3-TRANSACTIVATED PROTEIN 1. [RefSeq;Acc:NM_019048]
0.0339667	AQR	1259	0.137332	0.247332741
0.0340138	ADCK1	1651	0.142333	0.238973393	AARF DOMAIN CONTAINING KINASE 1. [RefSeq;Acc:NM_020421]
	ADCK2	1652			AARF DOMAIN CONTAINING KINASE 2; PUTATIVE UBIQUINONE BIOSYNTHESIS PROTEIN AARF. [RefSeq;Acc:NM_052853]
	CABC1	1650			"CHAPERONE-ACTIVITY OF BC1 COMPLEX-LIKE, MITOCHONDRIAL PRECURSOR (CHAPERONE-ABC1-LIKE). [SWISSPROT;Acc:Q8NI60]"
0.0340698	SNRPB2	1104	0.135722	0.251026363	"U2 SMALL NUCLEAR RIBONUCLEOPROTEIN B"". [SWISSPROT;Acc:P08579]"
0.0341617	KCMF1	493	0.12454	0.274303035	"POTASSIUM CHANNEL MODULATORY FACTOR 1; POTASSIUM CHANNEL MODULATORY FACTOR; DIFFERENTIALLY EXPRESSED IN BRANCHING TUBULOGENESIS 91; ZINC FINGER, ZZ DOMAIN CONTAINING 1. [RefSeq;Acc:NM_020122]"
0.0341846	SPTBN2	592	0.126926	0.269327009	"SPECTRIN BETA CHAIN, BRAIN 2 (SPECTRIN, NON-ERYTHROID BETA CHAIN 2) (BETA-III SPECTRIN). [SWISSPROT;Acc:O15020]"
0.0341996	MARCH8	1874	0.146922	0.232773853	CELLULAR MODULATOR OF IMMUNE RECOGNITION. [RefSeq;Acc:NM_145021]
0.0342505	TCP11	2124	0.150141	0.228122232	T-COMPLEX 11. [RefSeq;Acc:NM_018679]
0.034272	no value	373	0.122748	0.279206179
0.034279	GSK3B	1378	0.140116	0.244647292	GLYCOGEN SYNTHASE KINASE-3 BETA (EC 2.7.1.37) (GSK-3 BETA). [SWISSPROT;Acc:P49841]
0.0342868	CSE1L	1072	0.135906	0.252283196	IMPORTIN-ALPHA RE-EXPORTER (CHROMOSOME SEGREGATION 1-LIKE PROTEIN) (CELLULAR APOPTOSIS SUSCEPTIBILITY PROTEIN). [SWISSPROT;Acc:P55060]
0.0342893	NKIRAS2	1272	0.139064	0.246572082	I-KAPPA-B-INTERACTING RAS-LIKE PROTEIN 2. [RefSeq;Acc:NM_017595]
0.0343037	C20orf42	2511	0.159725	0.214767256
0.0343914	TMBIM4	2154	0.151289	0.227322542	Z-PROTEIN (PROTEIN CGI-119) (S1R PROTEIN). [SWISSPROT;Acc:Q9HC24]
0.0344025	PCDH15	2358	0.156164	0.220297252	PROTOCADHERIN 15 PRECURSOR. [SWISSPROT;Acc:Q96QU1]
0.0344093	MLYCD	831	0.131824	0.261024548	"MALONYL-COA DECARBOXYLASE, MITOCHONDRIAL PRECURSOR (EC 4.1.1.9) (MCD). [SWISSPROT;Acc:O95822]"
0.0344183	PDCL	1054	0.136218	0.252670719	PHOSDUCIN-LIKE PROTEIN (PHLP). [SWISSPROT;Acc:Q13371]
0.0344183	RAD52	1055	0.136218	0.252670719	DNA REPAIR PROTEIN RAD52 HOMOLOG. [SWISSPROT;Acc:P43351]
0.0344618	no value	492	0.125634	0.274303135
	ARFGAP3	491			ADP-RIBOSYLATION FACTOR GTPASE-ACTIVATING PROTEIN 3 (ARF GAP 3). [SWISSPROT;Acc:Q9NP61]
	CHCHD6	490
0.0345092	PIK3C2A	881	0.132688	0.260077776	"PHOSPHOINOSITIDE-3-KINASE, CLASS 2, ALPHA POLYPEPTIDE; C2-CONTAINING PHOSPHATIDYLINOSITOL KINASE. [RefSeq;Acc:NM_002645]"
0.0346049	SETD3	2436	0.159272	0.2172692
0.0348108	SCOC	931	0.135208	0.257461097	SHORT COILED-COIL PROTEIN; SHORT COILED COIL PROTEIN. [RefSeq;Acc:NM_032547]
0.0349396	UBE2W	1078	0.138505	0.252262373
0.0349473	ABT1	987	0.136958	0.255168008	ACTIVATOR OF BASAL TRANSCRIPTION 1; TATA-BINDING PROTEIN-BINDING PROTEIN; BASAL TRANSCRIPTIONAL ACTIVATOR. [RefSeq;Acc:NM_013375]
0.0349547	SLC37A2	912	0.135465	0.258034917
0.0349958	SRPK2	1338	0.142675	0.245283336	SFRS PROTEIN KINASE 2 ISOFORM B. [RefSeq;Acc:NM_182691]
0.0350787	AMMECR1	2177	0.154573	0.226939375	AMMECR1 PROTEIN. [RefSeq;Acc:NM_015365]
	RAE1	2176			MRNA-ASSOCIATED PROTEIN MRNP 41 (RAE1 PROTEIN HOMOLOG). [SWISSPROT;Acc:P78406]
	SCYL1	2174			SCY1-LIKE 1; TELOMERASE REGULATION-ASSOCIATED PROTEIN; HT019 PROTEIN; TELOMERASE REGULATION-ASSOCIATED PROTEIN; N-TERMINAL KINASE-LIKE PROTEIN; TERATOMA-ASSOCIATED TYROSINE KINASE; N-TERMINAL KINASE-LIKE. [RefSeq;Acc:NM_020680]
	TMF1	2175			TATA ELEMENT MODULATORY FACTOR (TMF). [SWISSPROT;Acc:P82094]
0.035086	NEK1	1690	0.147362	0.238093946	SERINE/THREONINE-PROTEIN KINASE NEK1 (EC 2.7.1.37) (NIMA-RELATED PROTEIN KINASE 1) (NY-REN-55 ANTIGEN). [SWISSPROT;Acc:Q96PY6]
0.0355659	PRSS7	276	0.116699	0.304766108	ENTEROPEPTIDASE PRECURSOR (EC 3.4.21.9) (ENTEROKINASE). [SWISSPROT;Acc:P98073]
0.0355674	RAB11FIP2	767	0.134909	0.263639935
0.035571	HOXB5	2979	0.254881	0.139559245	HOMEOBOX PROTEIN HOX-B5 (HOX-2A) (HHO.C10) (HU-1). [SWISSPROT;Acc:P09067]
0.0356563	CLGN	1049	0.14106	0.252773997	CALMEGIN PRECURSOR. [SWISSPROT;Acc:O14967]
0.035822	SMOC2	660	0.134108	0.267113073	SECRETED MODULAR CALCIUM-BINDING PROTEIN 2; SMOOTH MUSCLE ASSOCIATED PROTEIN 2. [RefSeq;Acc:NM_022138]
0.0358609	LRRC4B	540	0.13229	0.271077935
0.0359383	SCAMP3	2654	0.171181	0.209943276	SECRETORY CARRIER-ASSOCIATED MEMBRANE PROTEIN 3. [SWISSPROT;Acc:O14828]

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/