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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Hugo final measured Rank Gene expected description
Results: HTML CSV LaTeX Showing element 3158 to 3206 of 3206 in total
Hugo
final
measured
Rank
expected
description
ZC3H12A 0.227823074 0.0282774 2143 0.12412
ZC3H12C 0.227823377 0.0218584 2141 0.0959445
ZC3H14 0.344195075 0.200368 163 0.582135 NUCLEAR PROTEIN UKP68. [RefSeq;Acc:NM_024824]
ZCCHC4 0.229451425 0.0584321 2069 0.25466
ZCCHC7 0.223177651 0.0929892 2250 0.41666
ZCCHC8 0.264498255 0.0385694 741 0.145821
ZEB1 0.216721904 0.0329569 2456 0.15207 TRANSCRIPTION FACTOR 8 (NIL-2-A ZINC FINGER PROTEIN) (NEGATIVE REGULATOR OF IL2). [SWISSPROT;Acc:P37275]
ZEB2 0.216721134 0.0271894 2457 0.125458 ZINC FINGER HOMEOBOX PROTEIN 1B (SMAD INTERACTING PROTEIN 1) (SMADIP1) (HRIHFB2411). [SWISSPROT;Acc:O60315]
ZFAND1 0.252073432 0.0370737 1081 0.147075
ZFHX3 0.239052853 0.0721691 1640 0.301896 ALPHA-FETOPROTEIN ENHANCER BINDING PROTEIN (AT MOTIF-BINDING FACTOR) (AT-BINDING TRANSCRIPTION FACTOR 1). [SWISSPROT;Acc:Q15911]
ZFPL1 0.245725029 0.0418885 1313 0.170469 ZINC FINGER PROTEIN-LIKE 1; ZINC-FINGER PROTEIN IN MEN1 REGION. [RefSeq;Acc:NM_006782]
ZIC1 0.269091879 0.272286 603 1.01187 ZINC FINGER PROTEIN ZIC 1 (ZINC FINGER PROTEIN OF THE CEREBELLUM 1). [SWISSPROT;Acc:Q15915]
ZIC2 0.269112703 0.307359 599 1.14212 ZINC FINGER PROTEIN ZIC 2 (ZINC FINGER PROTEIN OF THE CEREBELLUM 2). [SWISSPROT;Acc:O95409]
ZIC3 0.269105031 0.25098 600 0.932647 ZINC FINGER PROTEIN ZIC 3 (ZINC FINGER PROTEIN OF THE CEREBELLUM 3). [SWISSPROT;Acc:O60481]
ZIC4 0.268844618 0.0906044 613 0.337014 ZINC FINGER PROTEIN ZIC 4 (ZINC FINGER PROTEIN OF THE CEREBELLUM 4) (FRAGMENT). [SWISSPROT;Acc:Q8N9L1]
ZMAT2 0.275611646 0.0394844 456 0.143261
ZMIZ1 0.267839193 0.204901 649 0.765015 RETINOIC ACID INDUCED 17; PIAS-LIKE PROTEIN HZIMP10. [RefSeq;Acc:NM_020338]
ZMIZ2 0.267833365 0.170567 652 0.63684
ZMPSTE24 0.21708522 0.205647 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 0.26467581 0.0311669 731 0.117755 ZINC FINGER PROTEIN 198 (FUSED IN MYELOPROLIFERATIVE DISORDERS PROTEIN) (REARRANGED IN ATYPICAL MYELOPROLIFERATIVE DISORDER PROTEIN). [SWISSPROT;Acc:Q9UBW7]
ZMYM3 0.264675936 0.030934 730 0.116875 ZINC FINGER PROTEIN 261 (DXS6673E PROTEIN). [SWISSPROT;Acc:Q14202]
ZMYM4 0.264676099 0.0398851 727 0.150694 ZINC FINGER PROTEIN 262; CELL DEATH INHIBITING RNA. [RefSeq;Acc:NM_005095]
ZMYM6 0.264677534 0.0317441 720 0.119935 ZINC FINGER PROTEIN 258. [RefSeq;Acc:NM_145310]
ZMYND11 0.262024728 0.0552487 789 0.210853 ADENOVIRUS 5 E1A-BINDING PROTEIN (BS69 PROTEIN). [SWISSPROT;Acc:Q15326]
ZMYND8 0.261998433 0.0371202 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 0.19345792 0.158934 2828 0.821543 ZINC FINGER PROTEIN 174 (AW-1). [SWISSPROT;Acc:Q15697]
ZNF18 0.193515925 0.164415 2826 0.84962 ZINC FINGER PROTEIN 18 (ZINC FINGER PROTEIN KOX11) (FRAGMENT). [SWISSPROT;Acc:P17022]
ZNF207 0.239178691 0.0769103 1637 0.32156 ZINC FINGER PROTEIN 207. [SWISSPROT;Acc:O43670]
ZNF213 0.193535095 0.166266 2818 0.8591 ZINC FINGER PROTEIN 213 (PUTATIVE TRANSCRIPTION FACTOR CR53). [SWISSPROT;Acc:O14771]
ZNF215 0.193516584 0.164486 2825 0.849984 ZINC FINGER PROTEIN 215 (BWSCR2 ASSOCIATED ZINC-FINGER PROTEIN 2) (BAZ 2). [SWISSPROT;Acc:Q9UL58]
ZNF232 0.193531379 0.16591 2820 0.857277 ZINC FINGER PROTEIN 232. [SWISSPROT;Acc:Q9UNY5]
ZNF24 0.193520363 0.164842 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 0.245085879 0.0726736 1356 0.296523 ZINC-FINGER PROTEIN ZPR1 (ZINC FINGER PROTEIN 259). [SWISSPROT;Acc:O75312]
ZNF274 0.19354132 0.166977 2817 0.862746 ZINC FINGER PROTEIN 274 (ZINC FINGER PROTEIN SP2114) (ZINC FINGER PROTEIN HFB101) (ZINC FINGER PROTEIN ZFP2) (ZF2). [SWISSPROT;Acc:Q96GC6]
ZNF289 0.274303236 0.02648 489 0.0965355 "ZINC FINGER PROTEIN 289, ID1 REGULATED; LIKELY ORTHOLOG OF MOUSE ZFP289. [RefSeq;Acc:NM_032389]"
ZNF394 0.193534676 0.166195 2819 0.858735 ZINC FINGER PROTEIN 99. [RefSeq;Acc:NM_032164]
ZNF444 0.193971485 0.225841 2816 1.1643 ZINC FINGER PROTEIN 444; ENDOTHELIAL ZINC FINGER PROTEIN 2. [RefSeq;Acc:NM_018337]
ZNF449 0.193522393 0.164985 2822 0.852537
ZNF496 0.193516584 0.164486 2824 0.849984
ZNF503 0.269104872 0.0700114 601 0.260164
ZNF547 0.119322081 0.0250043 3025 0.209553 SEDLIN. [SWISSPROT;Acc:O14582]
ZNF593 0.248333929 0.130571 1205 0.525788 ZINC FINGER PROTEIN T86. [SWISSPROT;Acc:O00488]
ZNF622 0.246000406 0.0473076 1288 0.192307 ZINC FINGER-LIKE PROTEIN 9. [RefSeq;Acc:NM_033414]
ZNF703 0.26910439 0.0897926 602 0.333672
ZNHIT3 0.278410061 0.0671887 399 0.24133 THYROID RECEPTOR INTERACTING PROTEIN 3 (TRIP-3) (FRAGMENT). [SWISSPROT;Acc:Q15649]
ZNRD1 0.228266219 0.193407 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 0.242682535 0.0271819 1503 0.112006 ZUOTIN RELATED FACTOR-1 (M-PHASE PHOSPHOPROTEIN 11). [SWISSPROT;Acc:Q99543]
ZSCAN12 0.193530958 0.165839 2821 0.856912 ZINC FINGER PROTEIN 305. [SWISSPROT;Acc:O43309]
ZYG11B 0.213427314 0.0789696 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
- http://analysis.yellowcouch.org/