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 measured final Gene Rank description expected
Results: HTML CSV LaTeX Showing element 3158 to 3206 of 3206 in total
Hugo
measured
final
Rank
description
expected
ZC3H12A 0.0282774 0.227823074 2143 0.12412
ZC3H12C 0.0218584 0.227823377 2141 0.0959445
ZC3H14 0.200368 0.344195075 163 NUCLEAR PROTEIN UKP68. [RefSeq;Acc:NM_024824] 0.582135
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 TRANSCRIPTION FACTOR 8 (NIL-2-A ZINC FINGER PROTEIN) (NEGATIVE REGULATOR OF IL2). [SWISSPROT;Acc:P37275] 0.15207
ZEB2 0.0271894 0.216721134 2457 ZINC FINGER HOMEOBOX PROTEIN 1B (SMAD INTERACTING PROTEIN 1) (SMADIP1) (HRIHFB2411). [SWISSPROT;Acc:O60315] 0.125458
ZFAND1 0.0370737 0.252073432 1081 0.147075
ZFHX3 0.0721691 0.239052853 1640 ALPHA-FETOPROTEIN ENHANCER BINDING PROTEIN (AT MOTIF-BINDING FACTOR) (AT-BINDING TRANSCRIPTION FACTOR 1). [SWISSPROT;Acc:Q15911] 0.301896
ZFPL1 0.0418885 0.245725029 1313 ZINC FINGER PROTEIN-LIKE 1; ZINC-FINGER PROTEIN IN MEN1 REGION. [RefSeq;Acc:NM_006782] 0.170469
ZIC1 0.272286 0.269091879 603 ZINC FINGER PROTEIN ZIC 1 (ZINC FINGER PROTEIN OF THE CEREBELLUM 1). [SWISSPROT;Acc:Q15915] 1.01187
ZIC2 0.307359 0.269112703 599 ZINC FINGER PROTEIN ZIC 2 (ZINC FINGER PROTEIN OF THE CEREBELLUM 2). [SWISSPROT;Acc:O95409] 1.14212
ZIC3 0.25098 0.269105031 600 ZINC FINGER PROTEIN ZIC 3 (ZINC FINGER PROTEIN OF THE CEREBELLUM 3). [SWISSPROT;Acc:O60481] 0.932647
ZIC4 0.0906044 0.268844618 613 ZINC FINGER PROTEIN ZIC 4 (ZINC FINGER PROTEIN OF THE CEREBELLUM 4) (FRAGMENT). [SWISSPROT;Acc:Q8N9L1] 0.337014
ZMAT2 0.0394844 0.275611646 456 0.143261
ZMIZ1 0.204901 0.267839193 649 RETINOIC ACID INDUCED 17; PIAS-LIKE PROTEIN HZIMP10. [RefSeq;Acc:NM_020338] 0.765015
ZMIZ2 0.170567 0.267833365 652 0.63684
ZMPSTE24 0.205647 0.21708522 2448 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] 0.94731
ZMYM2 0.0311669 0.26467581 731 ZINC FINGER PROTEIN 198 (FUSED IN MYELOPROLIFERATIVE DISORDERS PROTEIN) (REARRANGED IN ATYPICAL MYELOPROLIFERATIVE DISORDER PROTEIN). [SWISSPROT;Acc:Q9UBW7] 0.117755
ZMYM3 0.030934 0.264675936 730 ZINC FINGER PROTEIN 261 (DXS6673E PROTEIN). [SWISSPROT;Acc:Q14202] 0.116875
ZMYM4 0.0398851 0.264676099 727 ZINC FINGER PROTEIN 262; CELL DEATH INHIBITING RNA. [RefSeq;Acc:NM_005095] 0.150694
ZMYM6 0.0317441 0.264677534 720 ZINC FINGER PROTEIN 258. [RefSeq;Acc:NM_145310] 0.119935
ZMYND11 0.0552487 0.262024728 789 ADENOVIRUS 5 E1A-BINDING PROTEIN (BS69 PROTEIN). [SWISSPROT;Acc:Q15326] 0.210853
ZMYND8 0.0371202 0.261998433 809 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] 0.141681
ZNF174 0.158934 0.19345792 2828 ZINC FINGER PROTEIN 174 (AW-1). [SWISSPROT;Acc:Q15697] 0.821543
ZNF18 0.164415 0.193515925 2826 ZINC FINGER PROTEIN 18 (ZINC FINGER PROTEIN KOX11) (FRAGMENT). [SWISSPROT;Acc:P17022] 0.84962
ZNF207 0.0769103 0.239178691 1637 ZINC FINGER PROTEIN 207. [SWISSPROT;Acc:O43670] 0.32156
ZNF213 0.166266 0.193535095 2818 ZINC FINGER PROTEIN 213 (PUTATIVE TRANSCRIPTION FACTOR CR53). [SWISSPROT;Acc:O14771] 0.8591
ZNF215 0.164486 0.193516584 2825 ZINC FINGER PROTEIN 215 (BWSCR2 ASSOCIATED ZINC-FINGER PROTEIN 2) (BAZ 2). [SWISSPROT;Acc:Q9UL58] 0.849984
ZNF232 0.16591 0.193531379 2820 ZINC FINGER PROTEIN 232. [SWISSPROT;Acc:Q9UNY5] 0.857277
ZNF24 0.164842 0.193520363 2823 ZINC FINGER PROTEIN 24 (ZINC FINGER PROTEIN 191) (ZINC FINGER PROTEIN KOX17) (RETINOIC ACID SUPPRESSION PROTEIN A) (RSG-A). [SWISSPROT;Acc:P17028] 0.851807
ZNF259 0.0726736 0.245085879 1356 ZINC-FINGER PROTEIN ZPR1 (ZINC FINGER PROTEIN 259). [SWISSPROT;Acc:O75312] 0.296523
ZNF274 0.166977 0.19354132 2817 ZINC FINGER PROTEIN 274 (ZINC FINGER PROTEIN SP2114) (ZINC FINGER PROTEIN HFB101) (ZINC FINGER PROTEIN ZFP2) (ZF2). [SWISSPROT;Acc:Q96GC6] 0.862746
ZNF289 0.02648 0.274303236 489 "ZINC FINGER PROTEIN 289, ID1 REGULATED; LIKELY ORTHOLOG OF MOUSE ZFP289. [RefSeq;Acc:NM_032389]" 0.0965355
ZNF394 0.166195 0.193534676 2819 ZINC FINGER PROTEIN 99. [RefSeq;Acc:NM_032164] 0.858735
ZNF444 0.225841 0.193971485 2816 ZINC FINGER PROTEIN 444; ENDOTHELIAL ZINC FINGER PROTEIN 2. [RefSeq;Acc:NM_018337] 1.1643
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 SEDLIN. [SWISSPROT;Acc:O14582] 0.209553
ZNF593 0.130571 0.248333929 1205 ZINC FINGER PROTEIN T86. [SWISSPROT;Acc:O00488] 0.525788
ZNF622 0.0473076 0.246000406 1288 ZINC FINGER-LIKE PROTEIN 9. [RefSeq;Acc:NM_033414] 0.192307
ZNF703 0.0897926 0.26910439 602 0.333672
ZNHIT3 0.0671887 0.278410061 399 THYROID RECEPTOR INTERACTING PROTEIN 3 (TRIP-3) (FRAGMENT). [SWISSPROT;Acc:Q15649] 0.24133
ZNRD1 0.193407 0.228266219 2110 "ZINC RIBBON DOMAIN CONTAINING, 1; TRANSCRIPTION-ASSOCIATED ZINC RIBBON PROTEIN; RNA POLYMERASE I SMALL SPECIFIC SUBUNIT RPA12. [RefSeq;Acc:NM_014596]" 0.847287
ZRF1 0.0271819 0.242682535 1503 ZUOTIN RELATED FACTOR-1 (M-PHASE PHOSPHOPROTEIN 11). [SWISSPROT;Acc:Q99543] 0.112006
ZSCAN12 0.165839 0.193530958 2821 ZINC FINGER PROTEIN 305. [SWISSPROT;Acc:O43309] 0.856912
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
- http://analysis.yellowcouch.org/