MK5 Microarray Data

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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expected	Gene	measured	Rank	Hugo	description	final

Results: HTML CSV LaTeX

Showing element 402 to 451 of 3206 in total

expected	measured	Rank	Hugo	description	final
0.145189	0.0322816	2293	TMOD1	TROPOMODULIN 1 (ERYTHROCYTE TROPOMODULIN) (E-TMOD). [SWISSPROT;Acc:P28289]	0.222341913
		2294	TNK2	ACTIVATED P21CDC42HS KINASE. [RefSeq;Acc:NM_005781]
0.145258	0.0311751	2539	DPP6	DIPEPTIDYL AMINOPEPTIDASE-LIKE PROTEIN 6 (DIPEPTIDYLPEPTIDASE VI) (DIPEPTIDYLPEPTIDASE 6) (DIPEPTIDYL PEPTIDASE IV LIKE PROTEIN) (DIPEPTIDYL AMINOPEPTIDASE-RELATED PROTEIN) (DPPX). [SWISSPROT;Acc:P42658]	0.214618816
0.145382	0.0253172	2904	SAP30	"SIN3 ASSOCIATED POLYPEPTIDE P30; SIN3-ASSOCIATED POLYPEPTIDE, 30KD. [RefSeq;Acc:NM_003864]"	0.174142604
0.145611	0.0368889	1036	CSDE1	UNR PROTEIN. [SWISSPROT;Acc:O75534]	0.25333869
0.145754	0.0322443	2334	RRS1	RIBOSOME BIOGENESIS REGULATORY PROTEIN HOMOLOG. [SWISSPROT;Acc:Q15050]	0.221224117
0.145821	0.0385694	740	SLMO2	PROTEIN C20ORF45 (CGI-107). [SWISSPROT;Acc:Q9Y3B1]	0.264498255
		741	ZCCHC8
		742	BBS7	BARDET-BIEDL SYNDROME 7 PROTEIN ISOFORM A; BBS2-LIKE 1. [RefSeq;Acc:NM_176824]
		743	HSDL2
0.146383	0.0314375	2528	no value	KERATIN ASSOCIATED PROTEIN 4-2; KERATIN ASSOCIATED PROTEIN 4.2. [RefSeq;Acc:NM_033062]	0.21476196
0.146476	0.0401445	502	CDV3		0.274068789
0.146714	0.0374644	978	DEGS1	SPHINGOLIPID DELTA 4 DESATURASE; MEMBRANE FATTY ACID (LIPID) DESATURASE; DIHYDROCERAMIDE DESATURASE. [RefSeq;Acc:NM_003676]	0.25535668
0.1468	0.0378274	924	no value	FATTY ACID DESATURASE 1; LINOLEOYL-COA DESATURASE (DELTA-6-DESATURASE)-LIKE 1; DELTA-5 DESATURASE; DELTA-5 FATTY ACID DESATURASE. [RefSeq;Acc:NM_013402]	0.257679837
0.146922	0.0341996	1874	MARCH8	CELLULAR MODULATOR OF IMMUNE RECOGNITION. [RefSeq;Acc:NM_145021]	0.232773853
0.146984	0.0378747	926	PGGT1B	GERANYLGERANYL TRANSFERASE TYPE I BETA SUBUNIT (EC 2.5.1.-) (TYPE I PROTEIN GERANYL-GERANYLTRANSFERASE BETA SUBUNIT) (GGTASE-I-BETA). [SWISSPROT;Acc:P53609]	0.257679067
0.147075	0.0370737	1081	ZFAND1		0.252073432
0.147123	0.0369154	1107	MTR	"5-METHYLTETRAHYDROFOLATE--HOMOCYSTEINE METHYLTRANSFERASE (EC 2.1.1.13) (METHIONINE SYNTHASE, VITAMIN-B12 DEPENDENT) (MS). [SWISSPROT;Acc:Q99707]"	0.250915221
0.147362	0.035086	1690	NEK1	SERINE/THREONINE-PROTEIN KINASE NEK1 (EC 2.7.1.37) (NIMA-RELATED PROTEIN KINASE 1) (NY-REN-55 ANTIGEN). [SWISSPROT;Acc:Q96PY6]	0.238093946
0.14739	0.0399967	534	no value	SMALL NUCLEAR RIBONUCLEOPROTEIN E (SNRNP-E) (SM PROTEIN E) (SM-E) (SME). [SWISSPROT;Acc:P08578]	0.271366443
0.147402	0.0385127	823	TANC1		0.261276645
		824	STARD3	MLN 64 PROTEIN (STAR-RELATED LIPID TRANSFER PROTEIN 3) (STARD3) (START DOMAIN-CONTAINING PROTEIN 3) (CAB1 PROTEIN). [SWISSPROT;Acc:Q14849]
		825	FAT	CADHERIN-RELATED TUMOR SUPPRESSOR HOMOLOG PRECURSOR (FAT PROTEIN HOMOLOG). [SWISSPROT;Acc:Q14517]
0.147618	0.0420473	340	SF3A3	SPLICING FACTOR 3A SUBUNIT 3 (SPLICEOSOME ASSOCIATED PROTEIN 61) (SAP 61) (SF3A60). [SWISSPROT;Acc:Q12874]	0.28483857
0.147992	0.0373336	1074	JUP	JUNCTION PLAKOGLOBIN (DESMOPLAKIN III). [SWISSPROT;Acc:P14923]	0.25226769
0.148106	0.0366317	1255	AURKA	SERINE/THREONINE KINASE 6 (EC 2.7.1.37) (SERINE/THREONINE KINASE 15) (AURORA/IPL1-RELATED KINASE 1) (AURORA-RELATED KINASE 1) (HARK1) (AURORA-A) (BREAST-TUMOR-AMPLIFIED KINASE). [SWISSPROT;Acc:O14965]	0.247334342
		1256	CYLD	"CYLINDROMATOSIS (TURBAN TUMOR SYNDROME); CYLINDROMATOSIS 1, TURBAN TUMOR SYNDROME. [RefSeq;Acc:NM_015247]"
0.148314	0.031831	2538	DPP10	DIPEPTIDYLPEPTIDASE 10; DIPEPTIDYL PEPTIDASE IV-RELATED PROTEIN 3. [RefSeq;Acc:NM_020868]	0.214618984
0.148317	0.0378287	991	FUT8	"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"	0.255053028
0.14849299999999999	0.0332619	2237	IDH3G	"ISOCITRATE DEHYDROGENASE [NAD] SUBUNIT GAMMA, MITOCHONDRIAL PRECURSOR (EC 1.1.1.41) (ISOCITRIC DEHYDROGENASE) (NAD+-SPECIFIC ICDH). [SWISSPROT;Acc:P51553]"	0.223996417
0.149118	0.0320251	2527	KRTAP4-4	KERATIN ASSOCIATED PROTEIN 4.4. [RefSeq;Acc:NM_032524]	0.214763476
0.149576	0.0319993	2561	MRPS18A	"28S RIBOSOMAL PROTEIN S18A, MITOCHONDRIAL PRECURSOR (MRP-S18-A) (MRPS18A) (MRP-S18-3). [SWISSPROT;Acc:Q9NVS2]"	0.213933385
0.150141	0.0342505	2124	TCP11	T-COMPLEX 11. [RefSeq;Acc:NM_018679]	0.228122232
0.150395	0.048504	197	POLI	"POLYMERASE (DNA DIRECTED) IOTA; RAD30 (S. CEREVISIAE) HOMOLOG B; POLYMERASE (DNA-DIRECTED), IOTA. [RefSeq;Acc:NM_007195]"	0.322510722
0.150694	0.0398851	727	ZMYM4	ZINC FINGER PROTEIN 262; CELL DEATH INHIBITING RNA. [RefSeq;Acc:NM_005095]	0.264676099
		728	COG3	CONSERVED OLIGOMERIC GOLGI COMPLEX COMPONENT 3 (VESICLE DOCKING PROTEIN SEC34 HOMOLOG) (P94). [SWISSPROT;Acc:Q96JB2]
0.150941	0.0364961	1550	no value	ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 7 (ADP-RIBOSYLATION FACTOR-LIKE PROTEIN LAK). [SWISSPROT;Acc:P56559]	0.241790501
0.151058	0.042516	357			0.281454805
0.151289	0.0343914	2154	TMBIM4	Z-PROTEIN (PROTEIN CGI-119) (S1R PROTEIN). [SWISSPROT;Acc:Q9HC24]	0.227322542
	0.0395402	814	EXDL2		0.261355419
0.151367	0.0404532	657	SLU7	STEP II SPLICING FACTOR SLU7. [RefSeq;Acc:NM_006425]	0.267252439
0.15167	0.036822	1495	no value	IMPORTIN 7; RAN-BINDING PROTEIN 7. [RefSeq;Acc:NM_006391]	0.242777082
		1496	ARFGEF2	BREFELDIN A-INHIBITED GUANINE NUCLEOTIDE-EXCHANGE PROTEIN 2 (BREFELDIN A-INHIBITED GEP 2). [SWISSPROT;Acc:Q9Y6D5]
0.151786	0.03829	1076	EXO1	"EXONUCLEASE 1 ISOFORM B; RAD2 NUCLEASE FAMILY MEMBER, HOMOLOG OF S. CEREVISIAE EXONUCLEASE 1. [RefSeq;Acc:NM_006027]"	0.252263055
0.1519	0.0313747	2723	no value		0.206548387
0.151924	0.0617004	70	HEYL	HAIRY/ENHANCER-OF-SPLIT RELATED WITH YRPW MOTIF-LIKE. [RefSeq;Acc:NM_014571]	0.406126748
0.151938	0.0381158	1110	WDR22		0.250864168
0.15207	0.0329569	2456	ZEB1	TRANSCRIPTION FACTOR 8 (NIL-2-A ZINC FINGER PROTEIN) (NEGATIVE REGULATOR OF IL2). [SWISSPROT;Acc:P37275]	0.216721904
0.152326	0.0319827	2650	VPS35	VACUOLAR PROTEIN SORTING 35 (VESICLE PROTEIN SORTING 35) (HVPS35) (MATERNAL-EMBRYONIC 3). [SWISSPROT;Acc:Q96QK1]	0.209962186
0.152533	0.0491097	201	PABPC4	POLYADENYLATE-BINDING PROTEIN 4 (POLY(A)-BINDING PROTEIN 4) (PABP 4) (INDUCIBLE POLY(A)-BINDING PROTEIN) (IPABP) (ACTIVATED-PLATELET PROTEIN-1) (APP-1). [SWISSPROT;Acc:Q13310]	0.321961149

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