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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expected Gene Rank measured Hugo description final
Results: HTML CSV LaTeX Showing element 1452 to 1501 of 3206 in total
expected
Rank
measured
Hugo
description
final
0.46643 1250 0.11539 no value BLOCK 23. [SPTREMBL;Acc:Q8NHW5] 0.247389748
0.466478 1132 0.116856 BUB1B MITOTIC CHECKPOINT SERINE/THREONINE-PROTEIN KINASE BUB1 BETA (EC 2.7.1.-) (HBUBR1) (MAD3/BUB1-RELATED PROTEIN KINASE) (MITOTIC CHECKPOINT KINASE MAD3L). [SWISSPROT;Acc:O60566] 0.250506991
0.467587 880 0.121609 DNM1L DYNAMIN 1-LIKE PROTEIN ISOFORM 3; DYNAMIN-LIKE PROTEIN. [RefSeq;Acc:NM_005690] 0.260077804
0.468539 597 0.126132 LMO7 LIM DOMAIN ONLY 7; ZINC-FINGER DOMAIN-CONTAINING PROTEIN; LOMP PROTEIN; F-BOX ONLY PROTEIN 20; F-BOX PROTEIN FBX20. [RefSeq;Acc:NM_005358] 0.269202777
0.468587 331 0.133623 GABPA GA BINDING PROTEIN ALPHA CHAIN (GABP-ALPHA SUBUNIT) (TRANSCRIPTION FACTOR E4TF1-60) (NUCLEAR RESPIRATORY FACTOR-2 SUBUNIT ALPHA). [SWISSPROT;Acc:Q06546] 0.28516156
0.46893 1266 0.115741 LSM8 U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM8. [SWISSPROT;Acc:O95777] 0.246819355
0.469849 2301 0.10445 CEP70 P10-BINDING PROTEIN. [RefSeq;Acc:NM_024491] 0.222305464
0.469919 364 0.131623 C16orf42 "C316G12.2 (NOVEL PROTEIN SIMILAR TO PREDICTED YEAST, WORM AND ARCHAE- BACTERIAL PROTEINS) (SIMILAR TO UND313) (S. CERVISIAE) (HYPOTHETICAL PROTEIN). [SPTREMBL;Acc:Q9UJK0]" 0.280097208
0.47006 1065 0.118754 C1orf179 HYPORTHETICAL PROTEIN MGC27169. [RefSeq;Acc:NM_176782] 0.252635834
0.470166 2729 0.0967095 GPT ALANINE AMINOTRANSFERASE (EC 2.6.1.2) (GLUTAMIC--PYRUVIC TRANSAMINASE) (GPT) (GLUTAMIC--ALANINE TRANSAMINASE). [SWISSPROT;Acc:P24298] 0.205692245
0.470177 2915 0.0815544 PRAF2 JM4 PROTEIN. [RefSeq;Acc:NM_007213] 0.173454678
0.471496 1398 0.11514 MEGF6 MEGF6 (FRAGMENT). [SPTREMBL;Acc:O75095] 0.244201435
0.471848 885 0.122677 LRRC1 LAP (LEUCINE-RICH REPEATS AND PDZ) AND NO PDZ PROTEIN. [RefSeq;Acc:NM_018214] 0.259992625
0.472359 939 0.121116 YIF1A YIP1 INTERACTING FACTOR HOMOLOG; YIP1P-INTERACTING FACTOR; PUTATIVE RAB5-INTERACTING PROTEIN; PUTATIVE TRANSMEMBRANE PROTEIN 54TMP. [RefSeq;Acc:NM_020470] 0.256406674
0.472418 2759 0.0957295 SAPS3 SPORULATION-INDUCED TRANSCRIPT 4-ASSOCIATED PROTEIN. [RefSeq;Acc:NM_018312] 0.202637283
0.472616 693 0.125547 GCDH "GLUTARYL-COA DEHYDROGENASE, MITOCHONDRIAL PRECURSOR (EC 1.3.99.7) (GCD). [SWISSPROT;Acc:Q92947]" 0.265642721
0.472937 1480 0.114912 NUP54 NUCLEOPORIN 54KDA; NUCLEOPORIN P54. [RefSeq;Acc:NM_017426] 0.24297528
0.47397 621 0.12721 CAPZA1 F-ACTIN CAPPING PROTEIN ALPHA-1 SUBUNIT (CAPZ ALPHA-1). [SWISSPROT;Acc:P52907] 0.268392514
0.474687 1510 0.11516 C19orf50 0.242601967
0.475276 2703 0.0986882 MGLL MONOGLYCERIDE LIPASE; LYSOPHOSPHOLIPASE-LIKE. [RefSeq;Acc:NM_007283] 0.207643979
0.475357 695 0.126275 MAP3K6 MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 6 (EC 2.7.1.-). [SWISSPROT;Acc:O95382] 0.265642454
0.475769 233 0.149853 FOSB PROTEIN FOSB (G0/G1 SWITCH REGULATORY PROTEIN 3). [SWISSPROT;Acc:P53539] 0.31497008
0.476127 1249 0.11779 RPLP0 60S ACIDIC RIBOSOMAL PROTEIN P0 (L10E). [SWISSPROT;Acc:P05388] 0.247391977
0.476394 1434 0.116077 U2AF1 SPLICING FACTOR U2AF 35 KDA SUBUNIT (U2 AUXILIARY FACTOR 35 KDA SUBUNIT) (U2 SNRNP AUXILIARY FACTOR SMALL SUBUNIT). [SWISSPROT;Acc:Q01081] 0.243657561
0.476584 1859 0.111248 GTPBP8 0.233427895
0.47704 983 0.12174 FBP2 "FRUCTOSE-1,6-BISPHOSPHATASE ISOZYME 2 (EC 3.1.3.11) (D-FRUCTOSE-1,6- BISPHOSPHATE 1-PHOSPHOHYDROLASE) (FBPASE). [SWISSPROT;Acc:O00757]" 0.255198725
0.478436 347 0.135144 no value 0.282470383
348 DYRK1A DUAL-SPECIFICITY TYROSINE-PHOSPHORYLATION REGULATED KINASE 1A (EC 2.7.1.-) (PROTEIN KINASE MINIBRAIN HOMOLOG) (MNBH) (HP86) (DUAL SPECIFICITY YAK1-RELATED KINASE). [SWISSPROT;Acc:Q13627]
349 ELP4 ELONGATION PROTEIN 4 HOMOLOG; PAX6 NEIGHBOR GENE; CHROMOSOME 11 OPEN READING FRAME 19. [RefSeq;Acc:NM_019040]
0.478487 414 0.13272 SALL2 SAL-LIKE PROTEIN 2 (ZINC FINGER PROTEIN SALL2) (HSAL2). [SWISSPROT;Acc:Q9Y467] 0.277374307
0.478695 454 0.132041 TBL2 TRANSDUCIN BETA-LIKE 2 PROTEIN (WS BETA-TRANSDUCIN REPEATS PROTEIN) (WS-BETATRP) (WILLIAMS-BEUREN SYNDROME CHROMOSOME REGION 13 PROTEIN). [SWISSPROT;Acc:Q9Y4P3] 0.275835344
0.479216 864 0.124733 FAU 40S RIBOSOMAL PROTEIN S30. [SWISSPROT;Acc:Q05472] 0.26028555
0.479632 2044 0.110371 POLR2I DNA-DIRECTED RNA POLYMERASE II 14.5 KDA POLYPEPTIDE (EC 2.7.7.6) (RPB9) (RPB14.5). [SWISSPROT;Acc:P36954] 0.230116006
0.480144 2805 0.0949294 ZBTB7B KRUPPEL-RELATED ZINC FINGER PROTEIN HCKROX. [RefSeq;Acc:NM_015872] 0.19771027
0.480256 188 0.157948 BCAR3 BREAST CANCER ANTIESTROGEN RESISTANCE 3. [RefSeq;Acc:NM_003567] 0.328882929
0.480838 661 0.128438 PFDN1 PREFOLDIN SUBUNIT 1. [SWISSPROT;Acc:O60925] 0.267112832
0.481506 232 0.151666 FOSL2 FOS-RELATED ANTIGEN 2. [SWISSPROT;Acc:P15408] 0.314982576
0.481532 2811 0.0949008 RPP25 0.197080983
0.482648 511 0.131932 CLK2 PROTEIN KINASE CLK2 (EC 2.7.1.-) (CDC-LIKE KINASE 2). [SWISSPROT;Acc:P49760] 0.273350351
0.482771 237 0.151819 RANBP6 RAN-GTP BINDING PROTEIN (FRAGMENT). [SPTREMBL;Acc:O60518] 0.31447415
0.482909 2699 0.100335 HNRNPL HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN L (HNRNP L). [SWISSPROT;Acc:P14866] 0.207772065
0.483626 3113 0.0444473 PSCD4 CYTOHESIN 4. [SWISSPROT;Acc:Q9UIA0] 0.091904281
0.483922 697 0.128497 EPS8L2 EPIDERMAL GROWTH FACTOR RECEPTOR PATHWAY SUBSTRATE 8-LIKE PROTEIN 2; EPS8-RELATED PROTEIN 2; EPIDERMAL GROWTH FACTOR RECEPTOR PATHWAY SUBSTRATE 8-RELATED PROTEIN 2. [RefSeq;Acc:NM_022772] 0.265532462
0.484077 417 0.13427 ATN1 ATROPHIN-1 (DENTATORUBRAL-PALLIDOLUYSIAN ATROPHY PROTEIN). [SWISSPROT;Acc:P54259] 0.277373228
0.484315 342 0.137665 DTNBP1 DYSTROBREVIN BINDING PROTEIN 1; DYSBINDIN. [RefSeq;Acc:NM_032122] 0.284246823
0.484673 3060 0.0510974 GNAI1 "GUANINE NUCLEOTIDE-BINDING PROTEIN G(I), ALPHA-1 SUBUNIT (ADENYLATE CYCLASE-INHIBITING G ALPHA PROTEIN). [SWISSPROT;Acc:P04898]" 0.105426545
3061 GNAI3 "GUANINE NUCLEOTIDE-BINDING PROTEIN G(K), ALPHA SUBUNIT (G(I) ALPHA-3). [SWISSPROT;Acc:P08754]"
0.484774 392 0.135061 no value 40S RIBOSOMAL PROTEIN S26. [SWISSPROT;Acc:P02383] 0.278606113
0.485287 1062 0.122601 PBX4 PRE-B-CELL LEUKEMIA TRANSCRIPTION FACTOR 4. [RefSeq;Acc:NM_025245] 0.252636069
0.485319 3170 0.0287078 CCT3 "T-COMPLEX PROTEIN 1, GAMMA SUBUNIT (TCP-1-GAMMA) (CCT-GAMMA). [SWISSPROT;Acc:P49368]" 0.059152434

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/