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 Rank Gene expected description final measured
Results: HTML CSV LaTeX Showing element 3158 to 3206 of 3206 in total
Hugo
Rank
expected
description
final
measured
ZC3H12A 2143 0.12412 0.227823074 0.0282774
ZC3H12C 2141 0.0959445 0.227823377 0.0218584
ZC3H14 163 0.582135 NUCLEAR PROTEIN UKP68. [RefSeq;Acc:NM_024824] 0.344195075 0.200368
ZCCHC4 2069 0.25466 0.229451425 0.0584321
ZCCHC7 2250 0.41666 0.223177651 0.0929892
ZCCHC8 741 0.145821 0.264498255 0.0385694
ZEB1 2456 0.15207 TRANSCRIPTION FACTOR 8 (NIL-2-A ZINC FINGER PROTEIN) (NEGATIVE REGULATOR OF IL2). [SWISSPROT;Acc:P37275] 0.216721904 0.0329569
ZEB2 2457 0.125458 ZINC FINGER HOMEOBOX PROTEIN 1B (SMAD INTERACTING PROTEIN 1) (SMADIP1) (HRIHFB2411). [SWISSPROT;Acc:O60315] 0.216721134 0.0271894
ZFAND1 1081 0.147075 0.252073432 0.0370737
ZFHX3 1640 0.301896 ALPHA-FETOPROTEIN ENHANCER BINDING PROTEIN (AT MOTIF-BINDING FACTOR) (AT-BINDING TRANSCRIPTION FACTOR 1). [SWISSPROT;Acc:Q15911] 0.239052853 0.0721691
ZFPL1 1313 0.170469 ZINC FINGER PROTEIN-LIKE 1; ZINC-FINGER PROTEIN IN MEN1 REGION. [RefSeq;Acc:NM_006782] 0.245725029 0.0418885
ZIC1 603 1.01187 ZINC FINGER PROTEIN ZIC 1 (ZINC FINGER PROTEIN OF THE CEREBELLUM 1). [SWISSPROT;Acc:Q15915] 0.269091879 0.272286
ZIC2 599 1.14212 ZINC FINGER PROTEIN ZIC 2 (ZINC FINGER PROTEIN OF THE CEREBELLUM 2). [SWISSPROT;Acc:O95409] 0.269112703 0.307359
ZIC3 600 0.932647 ZINC FINGER PROTEIN ZIC 3 (ZINC FINGER PROTEIN OF THE CEREBELLUM 3). [SWISSPROT;Acc:O60481] 0.269105031 0.25098
ZIC4 613 0.337014 ZINC FINGER PROTEIN ZIC 4 (ZINC FINGER PROTEIN OF THE CEREBELLUM 4) (FRAGMENT). [SWISSPROT;Acc:Q8N9L1] 0.268844618 0.0906044
ZMAT2 456 0.143261 0.275611646 0.0394844
ZMIZ1 649 0.765015 RETINOIC ACID INDUCED 17; PIAS-LIKE PROTEIN HZIMP10. [RefSeq;Acc:NM_020338] 0.267839193 0.204901
ZMIZ2 652 0.63684 0.267833365 0.170567
ZMPSTE24 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] 0.21708522 0.205647
ZMYM2 731 0.117755 ZINC FINGER PROTEIN 198 (FUSED IN MYELOPROLIFERATIVE DISORDERS PROTEIN) (REARRANGED IN ATYPICAL MYELOPROLIFERATIVE DISORDER PROTEIN). [SWISSPROT;Acc:Q9UBW7] 0.26467581 0.0311669
ZMYM3 730 0.116875 ZINC FINGER PROTEIN 261 (DXS6673E PROTEIN). [SWISSPROT;Acc:Q14202] 0.264675936 0.030934
ZMYM4 727 0.150694 ZINC FINGER PROTEIN 262; CELL DEATH INHIBITING RNA. [RefSeq;Acc:NM_005095] 0.264676099 0.0398851
ZMYM6 720 0.119935 ZINC FINGER PROTEIN 258. [RefSeq;Acc:NM_145310] 0.264677534 0.0317441
ZMYND11 789 0.210853 ADENOVIRUS 5 E1A-BINDING PROTEIN (BS69 PROTEIN). [SWISSPROT;Acc:Q15326] 0.262024728 0.0552487
ZMYND8 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] 0.261998433 0.0371202
ZNF174 2828 0.821543 ZINC FINGER PROTEIN 174 (AW-1). [SWISSPROT;Acc:Q15697] 0.19345792 0.158934
ZNF18 2826 0.84962 ZINC FINGER PROTEIN 18 (ZINC FINGER PROTEIN KOX11) (FRAGMENT). [SWISSPROT;Acc:P17022] 0.193515925 0.164415
ZNF207 1637 0.32156 ZINC FINGER PROTEIN 207. [SWISSPROT;Acc:O43670] 0.239178691 0.0769103
ZNF213 2818 0.8591 ZINC FINGER PROTEIN 213 (PUTATIVE TRANSCRIPTION FACTOR CR53). [SWISSPROT;Acc:O14771] 0.193535095 0.166266
ZNF215 2825 0.849984 ZINC FINGER PROTEIN 215 (BWSCR2 ASSOCIATED ZINC-FINGER PROTEIN 2) (BAZ 2). [SWISSPROT;Acc:Q9UL58] 0.193516584 0.164486
ZNF232 2820 0.857277 ZINC FINGER PROTEIN 232. [SWISSPROT;Acc:Q9UNY5] 0.193531379 0.16591
ZNF24 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] 0.193520363 0.164842
ZNF259 1356 0.296523 ZINC-FINGER PROTEIN ZPR1 (ZINC FINGER PROTEIN 259). [SWISSPROT;Acc:O75312] 0.245085879 0.0726736
ZNF274 2817 0.862746 ZINC FINGER PROTEIN 274 (ZINC FINGER PROTEIN SP2114) (ZINC FINGER PROTEIN HFB101) (ZINC FINGER PROTEIN ZFP2) (ZF2). [SWISSPROT;Acc:Q96GC6] 0.19354132 0.166977
ZNF289 489 0.0965355 "ZINC FINGER PROTEIN 289, ID1 REGULATED; LIKELY ORTHOLOG OF MOUSE ZFP289. [RefSeq;Acc:NM_032389]" 0.274303236 0.02648
ZNF394 2819 0.858735 ZINC FINGER PROTEIN 99. [RefSeq;Acc:NM_032164] 0.193534676 0.166195
ZNF444 2816 1.1643 ZINC FINGER PROTEIN 444; ENDOTHELIAL ZINC FINGER PROTEIN 2. [RefSeq;Acc:NM_018337] 0.193971485 0.225841
ZNF449 2822 0.852537 0.193522393 0.164985
ZNF496 2824 0.849984 0.193516584 0.164486
ZNF503 601 0.260164 0.269104872 0.0700114
ZNF547 3025 0.209553 SEDLIN. [SWISSPROT;Acc:O14582] 0.119322081 0.0250043
ZNF593 1205 0.525788 ZINC FINGER PROTEIN T86. [SWISSPROT;Acc:O00488] 0.248333929 0.130571
ZNF622 1288 0.192307 ZINC FINGER-LIKE PROTEIN 9. [RefSeq;Acc:NM_033414] 0.246000406 0.0473076
ZNF703 602 0.333672 0.26910439 0.0897926
ZNHIT3 399 0.24133 THYROID RECEPTOR INTERACTING PROTEIN 3 (TRIP-3) (FRAGMENT). [SWISSPROT;Acc:Q15649] 0.278410061 0.0671887
ZNRD1 2110 0.847287 "ZINC RIBBON DOMAIN CONTAINING, 1; TRANSCRIPTION-ASSOCIATED ZINC RIBBON PROTEIN; RNA POLYMERASE I SMALL SPECIFIC SUBUNIT RPA12. [RefSeq;Acc:NM_014596]" 0.228266219 0.193407
ZRF1 1503 0.112006 ZUOTIN RELATED FACTOR-1 (M-PHASE PHOSPHOPROTEIN 11). [SWISSPROT;Acc:Q99543] 0.242682535 0.0271819
ZSCAN12 2821 0.856912 ZINC FINGER PROTEIN 305. [SWISSPROT;Acc:O43309] 0.193530958 0.165839
ZYG11B 2567 0.370007 0.213427314 0.0789696

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/