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	final	Rank	Gene	expected	description

Results: HTML CSV LaTeX

Showing element 3158 to 3206 of 3206 in total

Hugo	measured	final	Rank	expected	description
ZC3H12A	0.0282774	0.227823074	2143	0.12412
ZC3H12C	0.0218584	0.227823377	2141	0.0959445
ZC3H14	0.200368	0.344195075	163	0.582135	NUCLEAR PROTEIN UKP68. [RefSeq;Acc:NM_024824]
ZCCHC4	0.0584321	0.229451425	2069	0.25466
ZCCHC7	0.0929892	0.223177651	2250	0.41666
ZCCHC8	0.0385694	0.264498255	741	0.145821
ZEB1	0.0329569	0.216721904	2456	0.15207	TRANSCRIPTION FACTOR 8 (NIL-2-A ZINC FINGER PROTEIN) (NEGATIVE REGULATOR OF IL2). [SWISSPROT;Acc:P37275]
ZEB2	0.0271894	0.216721134	2457	0.125458	ZINC FINGER HOMEOBOX PROTEIN 1B (SMAD INTERACTING PROTEIN 1) (SMADIP1) (HRIHFB2411). [SWISSPROT;Acc:O60315]
ZFAND1	0.0370737	0.252073432	1081	0.147075
ZFHX3	0.0721691	0.239052853	1640	0.301896	ALPHA-FETOPROTEIN ENHANCER BINDING PROTEIN (AT MOTIF-BINDING FACTOR) (AT-BINDING TRANSCRIPTION FACTOR 1). [SWISSPROT;Acc:Q15911]
ZFPL1	0.0418885	0.245725029	1313	0.170469	ZINC FINGER PROTEIN-LIKE 1; ZINC-FINGER PROTEIN IN MEN1 REGION. [RefSeq;Acc:NM_006782]
ZIC1	0.272286	0.269091879	603	1.01187	ZINC FINGER PROTEIN ZIC 1 (ZINC FINGER PROTEIN OF THE CEREBELLUM 1). [SWISSPROT;Acc:Q15915]
ZIC2	0.307359	0.269112703	599	1.14212	ZINC FINGER PROTEIN ZIC 2 (ZINC FINGER PROTEIN OF THE CEREBELLUM 2). [SWISSPROT;Acc:O95409]
ZIC3	0.25098	0.269105031	600	0.932647	ZINC FINGER PROTEIN ZIC 3 (ZINC FINGER PROTEIN OF THE CEREBELLUM 3). [SWISSPROT;Acc:O60481]
ZIC4	0.0906044	0.268844618	613	0.337014	ZINC FINGER PROTEIN ZIC 4 (ZINC FINGER PROTEIN OF THE CEREBELLUM 4) (FRAGMENT). [SWISSPROT;Acc:Q8N9L1]
ZMAT2	0.0394844	0.275611646	456	0.143261
ZMIZ1	0.204901	0.267839193	649	0.765015	RETINOIC ACID INDUCED 17; PIAS-LIKE PROTEIN HZIMP10. [RefSeq;Acc:NM_020338]
ZMIZ2	0.170567	0.267833365	652	0.63684
ZMPSTE24	0.205647	0.21708522	2448	0.94731	CAAX PRENYL PROTEASE 1 HOMOLOG (EC 3.4.24.-) (PRENYL PROTEIN-SPECIFIC ENDOPROTEASE 1) (FARNESYLATED-PROTEINS CONVERTING ENZYME 1) (FACE-1) (ZINC METALLOPROTEINASE STE24 HOMOLOG). [SWISSPROT;Acc:O75844]
ZMYM2	0.0311669	0.26467581	731	0.117755	ZINC FINGER PROTEIN 198 (FUSED IN MYELOPROLIFERATIVE DISORDERS PROTEIN) (REARRANGED IN ATYPICAL MYELOPROLIFERATIVE DISORDER PROTEIN). [SWISSPROT;Acc:Q9UBW7]
ZMYM3	0.030934	0.264675936	730	0.116875	ZINC FINGER PROTEIN 261 (DXS6673E PROTEIN). [SWISSPROT;Acc:Q14202]
ZMYM4	0.0398851	0.264676099	727	0.150694	ZINC FINGER PROTEIN 262; CELL DEATH INHIBITING RNA. [RefSeq;Acc:NM_005095]
ZMYM6	0.0317441	0.264677534	720	0.119935	ZINC FINGER PROTEIN 258. [RefSeq;Acc:NM_145310]
ZMYND11	0.0552487	0.262024728	789	0.210853	ADENOVIRUS 5 E1A-BINDING PROTEIN (BS69 PROTEIN). [SWISSPROT;Acc:Q15326]
ZMYND8	0.0371202	0.261998433	809	0.141681	PROTEIN KINASE C BINDING PROTEIN 1 (RACK7) (CUTANEOUS T-CELL LYMPHOMA ASSOCIATED ANTIGEN SE14-3) (CTCL TUMOR ANTIGEN SE14-3) (ZINC FINGER MYND DOMAIN CONTAINING PROTEIN 8). [SWISSPROT;Acc:Q9ULU4]
ZNF174	0.158934	0.19345792	2828	0.821543	ZINC FINGER PROTEIN 174 (AW-1). [SWISSPROT;Acc:Q15697]
ZNF18	0.164415	0.193515925	2826	0.84962	ZINC FINGER PROTEIN 18 (ZINC FINGER PROTEIN KOX11) (FRAGMENT). [SWISSPROT;Acc:P17022]
ZNF207	0.0769103	0.239178691	1637	0.32156	ZINC FINGER PROTEIN 207. [SWISSPROT;Acc:O43670]
ZNF213	0.166266	0.193535095	2818	0.8591	ZINC FINGER PROTEIN 213 (PUTATIVE TRANSCRIPTION FACTOR CR53). [SWISSPROT;Acc:O14771]
ZNF215	0.164486	0.193516584	2825	0.849984	ZINC FINGER PROTEIN 215 (BWSCR2 ASSOCIATED ZINC-FINGER PROTEIN 2) (BAZ 2). [SWISSPROT;Acc:Q9UL58]
ZNF232	0.16591	0.193531379	2820	0.857277	ZINC FINGER PROTEIN 232. [SWISSPROT;Acc:Q9UNY5]
ZNF24	0.164842	0.193520363	2823	0.851807	ZINC FINGER PROTEIN 24 (ZINC FINGER PROTEIN 191) (ZINC FINGER PROTEIN KOX17) (RETINOIC ACID SUPPRESSION PROTEIN A) (RSG-A). [SWISSPROT;Acc:P17028]
ZNF259	0.0726736	0.245085879	1356	0.296523	ZINC-FINGER PROTEIN ZPR1 (ZINC FINGER PROTEIN 259). [SWISSPROT;Acc:O75312]
ZNF274	0.166977	0.19354132	2817	0.862746	ZINC FINGER PROTEIN 274 (ZINC FINGER PROTEIN SP2114) (ZINC FINGER PROTEIN HFB101) (ZINC FINGER PROTEIN ZFP2) (ZF2). [SWISSPROT;Acc:Q96GC6]
ZNF289	0.02648	0.274303236	489	0.0965355	"ZINC FINGER PROTEIN 289, ID1 REGULATED; LIKELY ORTHOLOG OF MOUSE ZFP289. [RefSeq;Acc:NM_032389]"
ZNF394	0.166195	0.193534676	2819	0.858735	ZINC FINGER PROTEIN 99. [RefSeq;Acc:NM_032164]
ZNF444	0.225841	0.193971485	2816	1.1643	ZINC FINGER PROTEIN 444; ENDOTHELIAL ZINC FINGER PROTEIN 2. [RefSeq;Acc:NM_018337]
ZNF449	0.164985	0.193522393	2822	0.852537
ZNF496	0.164486	0.193516584	2824	0.849984
ZNF503	0.0700114	0.269104872	601	0.260164
ZNF547	0.0250043	0.119322081	3025	0.209553	SEDLIN. [SWISSPROT;Acc:O14582]
ZNF593	0.130571	0.248333929	1205	0.525788	ZINC FINGER PROTEIN T86. [SWISSPROT;Acc:O00488]
ZNF622	0.0473076	0.246000406	1288	0.192307	ZINC FINGER-LIKE PROTEIN 9. [RefSeq;Acc:NM_033414]
ZNF703	0.0897926	0.26910439	602	0.333672
ZNHIT3	0.0671887	0.278410061	399	0.24133	THYROID RECEPTOR INTERACTING PROTEIN 3 (TRIP-3) (FRAGMENT). [SWISSPROT;Acc:Q15649]
ZNRD1	0.193407	0.228266219	2110	0.847287	"ZINC RIBBON DOMAIN CONTAINING, 1; TRANSCRIPTION-ASSOCIATED ZINC RIBBON PROTEIN; RNA POLYMERASE I SMALL SPECIFIC SUBUNIT RPA12. [RefSeq;Acc:NM_014596]"
ZRF1	0.0271819	0.242682535	1503	0.112006	ZUOTIN RELATED FACTOR-1 (M-PHASE PHOSPHOPROTEIN 11). [SWISSPROT;Acc:Q99543]
ZSCAN12	0.165839	0.193530958	2821	0.856912	ZINC FINGER PROTEIN 305. [SWISSPROT;Acc:O43309]
ZYG11B	0.0789696	0.213427314	2567	0.370007

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