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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Hugo	measured	Gene	expected	description	Rank	final

Results: HTML CSV LaTeX

Showing element 302 to 351 of 3206 in total

Hugo	measured	expected	description	Rank	final
no value	0.448528	1.82552	TGF BETA-INDUCIBLE NUCLEAR PROTEIN 1; HAIRY CELL LEUKEMIA PROTEIN 1. [RefSeq;Acc:NM_014886]	1316	0.24569876
	0.477897	2.0867	40S RIBOSOMAL PROTEIN S29. [SWISSPROT;Acc:P30054]	2084	0.229020463
	0.478004	2.27081	ALCOHOL DEHYDROGENASE CLASS III CHI CHAIN (EC 1.1.1.1) (GLUTATHIONE- DEPENDENT FORMALDEHYDE DEHYDROGENASE) (EC 1.2.1.1) (FDH). [SWISSPROT;Acc:P11766]	2619	0.210499337
	0.481793	1.95026	LAMIN B2. [SWISSPROT;Acc:Q03252]	1264	0.247040395
	0.482398	1.63545	BA395L14.12 (NOVEL PROTEIN SIMILAR TO SMALL NUCLEAR RIBONUCLEOPROTEIN POLYPEPTIDE A' (SNRPA1)). [SPTREMBL;Acc:Q9NU36]	313	0.294963466
	0.492676	1.87133	CASEIN KINASE II BETA CHAIN (CK II) (PHOSVITIN) (G5A). [SWISSPROT;Acc:P13862]	772	0.263275852
	0.505323	2.18834	60S RIBOSOMAL PROTEIN L12 LIKE PROTEIN. [SPTREMBL;Acc:O60886]	1989	0.230916128
	0.512064	2.39827	3-HYDROXYISOBUTYRYL-COENZYME A HYDROLASE. [RefSeq;Acc:NM_014362]	2566	0.213513908
	0.512921	2.22124	DJ999L4.1 (NOVEL PROTEIN SIMILAR TO RIBOSOMAL PROTEIN L12 (RPL12)). [SPTREMBL;Acc:Q9NQ02]	1988	0.230916515
	0.52666	1.98825	HISTONE DEACETYLASE 2 (HD2). [SWISSPROT;Acc:Q92769]	712	0.264886206
	0.527851	2.28589	60S RIBOSOMAL PROTEIN L12. [SWISSPROT;Acc:P30050]	1987	0.230917061
	0.533964	2.31472	NUCLEOSIDE DIPHOSPHATE KINASE B (EC 2.7.4.6) (NDK B) (NDP KINASE B) (NM23-H2) (C-MYC PURINE-BINDING TRANSCRIPTION FACTOR PUF). [SWISSPROT;Acc:P22392]	2009	0.230681897
	0.534301	1.96129	ATAXIN 2-BINDING PROTEIN. [SWISSPROT;Acc:Q9NWB1]	515	0.272423252
	0.539175	1.99055	ELAV-LIKE PROTEIN 3 (HU-ANTIGEN C) (HUC) (PARANEOPLASTIC CEREBELLAR DEGENERATION-ASSOCIATED ANTIGEN) (PARANEOPLASTIC LIMBIC ENCEPHALITIS ANTIGEN 21). [SWISSPROT;Acc:Q14576]	560	0.270867348
	0.539817	2.48653	ARSENICAL PUMP-DRIVING ATPASE (EC 3.6.3.16) (ARSENITE-TRANSLOCATING ATPASE) (ARSENICAL RESISTANCE ATPASE) (ARSENITE-TRANSPORTING ATPASE) (ARSA) (ASNA-I). [SWISSPROT;Acc:O43681]	2443	0.217096516
	0.541146	2.34239	60S RIBOSOMAL PROTEIN L10A (CSA-19). [SWISSPROT;Acc:P53025]	1979	0.231023015
	0.542979	2.61855		2707	0.207358653
	0.543161	2.35379	40S RIBOSOMAL PROTEIN S18 (KE-3) (KE3). [SWISSPROT;Acc:P25232]	1998	0.230760178
	0.549308	2.36366		1902	0.232397214
	0.563143	2.05361	SEVEN IN ABSENTIA HOMOLOG 1. [RefSeq;Acc:NM_003031]	499	0.274221006
	0.563839	2.36701	26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 12 (26S PROTEASOME REGULATORY SUBUNIT P55). [SWISSPROT;Acc:O00232]	1680	0.238207274
	0.572386	2.31408	IMPORTIN 4. [RefSeq;Acc:NM_024658]	1253	0.247349271
	0.596229	2.43411		1362	0.244947435
	0.61026	2.72155	GLUCOSAMINE--FRUCTOSE-6-PHOSPHATE AMINOTRANSFERASE [ISOMERIZING] 1 (EC 2.6.1.16) (HEXOSEPHOSPHATE AMINOTRANSFERASE 1) (D-FRUCTOSE-6- PHOSPHATE AMIDOTRANSFERASE 1) (GFAT 1) (GFAT1). [SWISSPROT;Acc:Q06210]	2231	0.224232515
	0.625831	2.00343	TRANSCRIPTION FACTOR BTF3 HOMOLOG 3. [SWISSPROT;Acc:Q13892]	247	0.312379769
	0.63284	2.72242	60S RIBOSOMAL PROTEIN L17 (L23). [SWISSPROT;Acc:P18621]	1899	0.232454948
	0.64348	2.79016	60S RIBOSOMAL PROTEIN L23 (L17). [SWISSPROT;Acc:P23131]	2014	0.230624767
	0.676836	2.7231	PROTEASOME SUBUNIT BETA TYPE 8 PRECURSOR (EC 3.4.25.1) (PROTEASOME COMPONENT C13) (MACROPAIN SUBUNIT C13) (MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT C13). [SWISSPROT;Acc:P28062]	1194	0.248553487
	0.694134	2.5522	"PRE-MRNA CLEAVAGE FACTOR I, 59 KDA SUBUNIT. [RefSeq;Acc:NM_024811]"	522	0.271974767
	0.704795	3.04081		1928	0.231778704
	0.707942	3.07604	"40S RIBOSOMAL PROTEIN S4, X ISOFORM (SINGLE COPY ABUNDANT MRNA PROTEIN) (SCR10). [SWISSPROT;Acc:P12750]"	2040	0.230147202
	0.743299	2.38318		251	0.311893772
	0.745512	3.26763	"PEROXISOMAL 3,2-TRANS-ENOYL-COA ISOMERASE (EC 5.3.3.8) (DODECENOYL-COA DELTA-ISOMERASE) (D3,D2-ENOYL-COA ISOMERASE) (DBI-RELATED PROTEIN 1) (DRS-1) (HEPATOCELLULAR CARCINOMA-ASSOCIATED ANTIGEN 88). [SWISSPROT;Acc:O75521]"	2119	0.228150678
	0.755644	2.42272	ALPHA-NAC PROTEIN. [SPTREMBL;Acc:Q9H009]	250	0.311899023
	0.788679	3.36493	60S RIBOSOMAL PROTEIN L9. [SWISSPROT;Acc:P32969]	1814	0.234381993
	0.788778	2.02915	TRANSCRIPTION FACTOR DP-1 (E2F DIMERIZATION PARTNER 1) (DRTF1- POLYPEPTIDE-1) (DRTF1). [SWISSPROT;Acc:Q14186]	85	0.388723357
	0.804734	2.57998	NASCENT-POLYPEPTIDE-ASSOCIATED COMPLEX ALPHA POLYPEPTIDE. [RefSeq;Acc:NM_005594]	249	0.311914821
	0.839834	4.39067	SMALL GLUTAMINE RICH PROTEIN WITH TETRATRICOPEPTIDE REPEATS 2. [RefSeq;Acc:NM_019072]	2852	0.191276958
	0.914796	2.37847		92	0.38461532
	1.02862	4.7857	KERATIN ASSOCIATED PROTEIN 9-4; KERATIN ASSOCIATED PROTEIN 9.4. [RefSeq;Acc:NM_033191]	2502	0.214936164
	1.03026	4.4602	60S RIBOSOMAL PROTEIN L10 (QM PROTEIN) (TUMOR SUPPRESSOR QM) (LAMININ RECEPTOR HOMOLOG). [SWISSPROT;Acc:P27635]	1981	0.230989642
	1.04135	4.48455	SUPPRESSOR OF TY 5 HOMOLOG; SUPPRESSOR OF TY (S.CEREVISIAE) 5 HOMOLOG. [RefSeq;Acc:NM_003169]	1906	0.23220836
	1.08194	3.53138	SPLICING FACTOR 3B SUBUNIT 3 (SPLICEOSOME ASSOCIATED PROTEIN 130) (SAP 130) (SF3B130) (PRE-MRNA SPLICING FACTOR SF3B 130 KDA SUBUNIT). [SWISSPROT;Acc:Q15393]	269	0.306378809
	1.24769	5.38515	C367G8.3 (NOVEL PROTEIN SIMILAR TO RPL23A (60S RIBOSOMAL PROTEIN L23A)) (60S RIBOSOMAL PROTEIN L23A LIKE). [SPTREMBL;Acc:Q9BR02]	1935	0.231690854
	1.27676	5.53686	PUTATIVE EUKARYOTIC TRANSLATION INITIATION FACTOR 1A (EIF-1A) (EIF- 4C). [SWISSPROT;Acc:O75642]	2016	0.230592791
	1.32362	5.71513	40S RIBOSOMAL PROTEIN S15 (RIG PROTEIN). [SWISSPROT;Acc:P11174]	1943	0.231599281
	1.40328	6.05655	60S RIBOSOMAL PROTEIN L23A. [SWISSPROT;Acc:P29316]	1934	0.231696263
	1.469	6.36963	40S RIBOSOMAL PROTEIN S2 (S4) (LLREP3 PROTEIN). [SWISSPROT;Acc:P15880]	2012	0.230625641
	3.66001	3.3348		4	1.097520091
AAK1	0.168547	0.60766	ADAPTOR-ASSOCIATED KINASE 1. [RefSeq;Acc:NM_014911]	423	0.277370569

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