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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Gene Hugo measured expected Rank final description
Results: HTML CSV LaTeX Showing element 3158 to 3206 of 3206 in total
Hugo
measured
expected
Rank
final
description
ZC3H12A 0.0282774 0.12412 2143 0.227823074
ZC3H12C 0.0218584 0.0959445 2141 0.227823377
ZC3H14 0.200368 0.582135 163 0.344195075 NUCLEAR PROTEIN UKP68. [RefSeq;Acc:NM_024824]
ZCCHC4 0.0584321 0.25466 2069 0.229451425
ZCCHC7 0.0929892 0.41666 2250 0.223177651
ZCCHC8 0.0385694 0.145821 741 0.264498255
ZEB1 0.0329569 0.15207 2456 0.216721904 TRANSCRIPTION FACTOR 8 (NIL-2-A ZINC FINGER PROTEIN) (NEGATIVE REGULATOR OF IL2). [SWISSPROT;Acc:P37275]
ZEB2 0.0271894 0.125458 2457 0.216721134 ZINC FINGER HOMEOBOX PROTEIN 1B (SMAD INTERACTING PROTEIN 1) (SMADIP1) (HRIHFB2411). [SWISSPROT;Acc:O60315]
ZFAND1 0.0370737 0.147075 1081 0.252073432
ZFHX3 0.0721691 0.301896 1640 0.239052853 ALPHA-FETOPROTEIN ENHANCER BINDING PROTEIN (AT MOTIF-BINDING FACTOR) (AT-BINDING TRANSCRIPTION FACTOR 1). [SWISSPROT;Acc:Q15911]
ZFPL1 0.0418885 0.170469 1313 0.245725029 ZINC FINGER PROTEIN-LIKE 1; ZINC-FINGER PROTEIN IN MEN1 REGION. [RefSeq;Acc:NM_006782]
ZIC1 0.272286 1.01187 603 0.269091879 ZINC FINGER PROTEIN ZIC 1 (ZINC FINGER PROTEIN OF THE CEREBELLUM 1). [SWISSPROT;Acc:Q15915]
ZIC2 0.307359 1.14212 599 0.269112703 ZINC FINGER PROTEIN ZIC 2 (ZINC FINGER PROTEIN OF THE CEREBELLUM 2). [SWISSPROT;Acc:O95409]
ZIC3 0.25098 0.932647 600 0.269105031 ZINC FINGER PROTEIN ZIC 3 (ZINC FINGER PROTEIN OF THE CEREBELLUM 3). [SWISSPROT;Acc:O60481]
ZIC4 0.0906044 0.337014 613 0.268844618 ZINC FINGER PROTEIN ZIC 4 (ZINC FINGER PROTEIN OF THE CEREBELLUM 4) (FRAGMENT). [SWISSPROT;Acc:Q8N9L1]
ZMAT2 0.0394844 0.143261 456 0.275611646
ZMIZ1 0.204901 0.765015 649 0.267839193 RETINOIC ACID INDUCED 17; PIAS-LIKE PROTEIN HZIMP10. [RefSeq;Acc:NM_020338]
ZMIZ2 0.170567 0.63684 652 0.267833365
ZMPSTE24 0.205647 0.94731 2448 0.21708522 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 0.117755 731 0.26467581 ZINC FINGER PROTEIN 198 (FUSED IN MYELOPROLIFERATIVE DISORDERS PROTEIN) (REARRANGED IN ATYPICAL MYELOPROLIFERATIVE DISORDER PROTEIN). [SWISSPROT;Acc:Q9UBW7]
ZMYM3 0.030934 0.116875 730 0.264675936 ZINC FINGER PROTEIN 261 (DXS6673E PROTEIN). [SWISSPROT;Acc:Q14202]
ZMYM4 0.0398851 0.150694 727 0.264676099 ZINC FINGER PROTEIN 262; CELL DEATH INHIBITING RNA. [RefSeq;Acc:NM_005095]
ZMYM6 0.0317441 0.119935 720 0.264677534 ZINC FINGER PROTEIN 258. [RefSeq;Acc:NM_145310]
ZMYND11 0.0552487 0.210853 789 0.262024728 ADENOVIRUS 5 E1A-BINDING PROTEIN (BS69 PROTEIN). [SWISSPROT;Acc:Q15326]
ZMYND8 0.0371202 0.141681 809 0.261998433 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 0.821543 2828 0.19345792 ZINC FINGER PROTEIN 174 (AW-1). [SWISSPROT;Acc:Q15697]
ZNF18 0.164415 0.84962 2826 0.193515925 ZINC FINGER PROTEIN 18 (ZINC FINGER PROTEIN KOX11) (FRAGMENT). [SWISSPROT;Acc:P17022]
ZNF207 0.0769103 0.32156 1637 0.239178691 ZINC FINGER PROTEIN 207. [SWISSPROT;Acc:O43670]
ZNF213 0.166266 0.8591 2818 0.193535095 ZINC FINGER PROTEIN 213 (PUTATIVE TRANSCRIPTION FACTOR CR53). [SWISSPROT;Acc:O14771]
ZNF215 0.164486 0.849984 2825 0.193516584 ZINC FINGER PROTEIN 215 (BWSCR2 ASSOCIATED ZINC-FINGER PROTEIN 2) (BAZ 2). [SWISSPROT;Acc:Q9UL58]
ZNF232 0.16591 0.857277 2820 0.193531379 ZINC FINGER PROTEIN 232. [SWISSPROT;Acc:Q9UNY5]
ZNF24 0.164842 0.851807 2823 0.193520363 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 0.296523 1356 0.245085879 ZINC-FINGER PROTEIN ZPR1 (ZINC FINGER PROTEIN 259). [SWISSPROT;Acc:O75312]
ZNF274 0.166977 0.862746 2817 0.19354132 ZINC FINGER PROTEIN 274 (ZINC FINGER PROTEIN SP2114) (ZINC FINGER PROTEIN HFB101) (ZINC FINGER PROTEIN ZFP2) (ZF2). [SWISSPROT;Acc:Q96GC6]
ZNF289 0.02648 0.0965355 489 0.274303236 "ZINC FINGER PROTEIN 289, ID1 REGULATED; LIKELY ORTHOLOG OF MOUSE ZFP289. [RefSeq;Acc:NM_032389]"
ZNF394 0.166195 0.858735 2819 0.193534676 ZINC FINGER PROTEIN 99. [RefSeq;Acc:NM_032164]
ZNF444 0.225841 1.1643 2816 0.193971485 ZINC FINGER PROTEIN 444; ENDOTHELIAL ZINC FINGER PROTEIN 2. [RefSeq;Acc:NM_018337]
ZNF449 0.164985 0.852537 2822 0.193522393
ZNF496 0.164486 0.849984 2824 0.193516584
ZNF503 0.0700114 0.260164 601 0.269104872
ZNF547 0.0250043 0.209553 3025 0.119322081 SEDLIN. [SWISSPROT;Acc:O14582]
ZNF593 0.130571 0.525788 1205 0.248333929 ZINC FINGER PROTEIN T86. [SWISSPROT;Acc:O00488]
ZNF622 0.0473076 0.192307 1288 0.246000406 ZINC FINGER-LIKE PROTEIN 9. [RefSeq;Acc:NM_033414]
ZNF703 0.0897926 0.333672 602 0.26910439
ZNHIT3 0.0671887 0.24133 399 0.278410061 THYROID RECEPTOR INTERACTING PROTEIN 3 (TRIP-3) (FRAGMENT). [SWISSPROT;Acc:Q15649]
ZNRD1 0.193407 0.847287 2110 0.228266219 "ZINC RIBBON DOMAIN CONTAINING, 1; TRANSCRIPTION-ASSOCIATED ZINC RIBBON PROTEIN; RNA POLYMERASE I SMALL SPECIFIC SUBUNIT RPA12. [RefSeq;Acc:NM_014596]"
ZRF1 0.0271819 0.112006 1503 0.242682535 ZUOTIN RELATED FACTOR-1 (M-PHASE PHOSPHOPROTEIN 11). [SWISSPROT;Acc:Q99543]
ZSCAN12 0.165839 0.856912 2821 0.193530958 ZINC FINGER PROTEIN 305. [SWISSPROT;Acc:O43309]
ZYG11B 0.0789696 0.370007 2567 0.213427314

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/