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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Rank Gene description measured expected Hugo final
Results: HTML CSV LaTeX Showing element 601 to 650 of 3206 in total
Rank
description
measured
expected
Hugo
final
601 0.0700114 0.260164 ZNF503 0.269104872
602 0.0897926 0.333672 ZNF703 0.26910439
603 ZINC FINGER PROTEIN ZIC 1 (ZINC FINGER PROTEIN OF THE CEREBELLUM 1). [SWISSPROT;Acc:Q15915] 0.272286 1.01187 ZIC1 0.269091879
604 HOMEOBOX PROTEIN OTX2. [SWISSPROT;Acc:P32243] 0.276018 1.02596 OTX2 0.26903388
605 HOMEOBOX PROTEIN OTX1. [SWISSPROT;Acc:P32242] 0.237139 0.88153 OTX1 0.269008429
606 CONE-ROD HOMEOBOX PROTEIN. [SWISSPROT;Acc:O43186] 0.226785 0.843068 CRX 0.268999654
607 LANTHIONINE SYNTHETASE C-LIKE PROTEIN 1; G PROTEIN-COUPLED RECEPTOR 69A; LANC (BACTERIAL LANTIBIOTIC SYNTHETASE COMPONENT C)-LIKE 1; LANC (BACTERIAL LANTIBIOTIC SYNTHETASE COMPONENT). [RefSeq;Acc:NM_006055] 0.0803201 0.29864 LANCL1 0.26895292
608 LANC LANTIBIOTIC SYNTHETASE COMPONENT C-LIKE 2; TESTIS-SPECIFIC ADRIAMYCIN SENSITIVITY PROTEIN; LANC (BACTERIAL LANTIBIOTIC SYNTHETASE COMPONENT C)-LIKE 2; G PROTEIN-COUPLED RECEPTOR 69B. [RefSeq;Acc:NM_018697] 0.0958474 0.356373 LANCL2 0.268952474
609 HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE (EC 2.4.2.8) (HGPRT) (HGPRTASE). [SWISSPROT;Acc:P00492] 0.34395 1.27889 HPRT1 0.268944163
610 DJ947L8.1.6 (NOVEL CUB AND SUSHI (SCR REPEAT) DOMAIN PROTEIN) (FRAGMENT). [SPTREMBL;Acc:Q9H4W2] 0.0586244 0.21806 CSMD1 0.268845272
611 CALCIPRESSIN 1 (DOWN SYNDROME CRITICAL REGION PROTEIN 1) (MYOCYTE- ENRICHED CALCINEURIN INTERACTING PROTEIN 1) (MCIP1) (ADAPT78). [SWISSPROT;Acc:P53805] 0.346654 1.28942 RCAN1 0.268844907
612 CALCIPRESSIN 2 (THYROID HORMONE-RESPONSIVE PROTEIN ZAKI-4) (DOWN SYNDROME CANDIDATE REGION 1-LIKE 1) (MYOCYTE-ENRICHED CALCINEURIN INTERACTING PROTEIN 2) (MCIP2). [SWISSPROT;Acc:Q14206] 0.281682 1.04775 RCAN2 0.268844667
613 ZINC FINGER PROTEIN ZIC 4 (ZINC FINGER PROTEIN OF THE CEREBELLUM 4) (FRAGMENT). [SWISSPROT;Acc:Q8N9L1] 0.0906044 0.337014 ZIC4 0.268844618
614 DJ947L8.1.1 (NOVEL CUB AND SUSHI (SCR REPEAT) DOMAIN PROTEIN) (FRAGMENT). [SPTREMBL;Acc:Q9H4V7] 0.090945 0.338281 no value 0.26884454
615 CALCIPRESSIN 3 (DOWN SYNDROME CANDIDATE REGION 1-LIKE PROTEIN 2) (MYOCYTE-ENRICHED CALCINEURIN INTERACTING PROTEIN 3) (MCIP3). [SWISSPROT;Acc:Q9UKA8] 0.279332 1.03901 RCAN3 0.268844381
616 P29ING4; CANDIDATE TUMOR SUPPRESSOR P33 ING1 HOMOLOG. [RefSeq;Acc:NM_016162] 0.0616259 0.229333 ING4 0.268717978
617 "SERINE/THREONINE PROTEIN PHOSPHATASE 2B CATALYTIC SUBUNIT, GAMMA ISOFORM (EC 3.1.3.16) (CALMODULIN-DEPENDENT CALCINEURIN A SUBUNIT, GAMMA ISOFORM) (CALCINEURIN, TESTIS-SPECIFIC CATALYTIC SUBUNIT) (CAM-PRP CATALYTIC SUBUNIT). [SWISSPROT;Acc:P48454]" 0.221484 0.824699 PPP3CC 0.26856344
618 "SERINE/THREONINE PROTEIN PHOSPHATASE 2B CATALYTIC SUBUNIT, BETA ISOFORM (EC 3.1.3.16) (CALMODULIN-DEPENDENT CALCINEURIN A SUBUNIT, BETA ISOFORM) (CAM-PRP CATALYTIC SUBUNIT). [SWISSPROT;Acc:P16299]" 0.232385 0.865296 PPP3CB 0.268561278
619 P PROTEIN (MELANOCYTE-SPECIFIC TRANSPORTER PROTEIN). [SWISSPROT;Acc:Q04671] 0.116815 0.43497 OCA2 0.268558751
620 "SERINE/THREONINE PROTEIN PHOSPHATASE 2B CATALYTIC SUBUNIT, ALPHA ISOFORM (EC 3.1.3.16) (CALMODULIN-DEPENDENT CALCINEURIN A SUBUNIT, ALPHA ISOFORM) (CAM-PRP CATALYTIC SUBUNIT). [SWISSPROT;Acc:Q08209]" 0.283215 1.05458 PPP3CA 0.268557151
621 F-ACTIN CAPPING PROTEIN ALPHA-1 SUBUNIT (CAPZ ALPHA-1). [SWISSPROT;Acc:P52907] 0.12721 0.47397 CAPZA1 0.268392514
622 SESTRIN 1 (P53-REGULATED PROTEIN PA26). [SWISSPROT;Acc:Q9Y6P5] 0.699473 2.60745 SESN1 0.268259411
623 CYTOCHROME P450 4F11 (EC 1.14.14.1) (CYPIVF11). [SWISSPROT;Acc:Q9HBI6] 0.113522 0.42318 CYP4F11 0.26825937
624 FLOTILLIN-1. [SWISSPROT;Acc:O75955] 0.11908 0.443899 FLOT1 0.268259221
625 0.102776 0.383122 CYP4F22 0.268259197
626 0.0869771 0.324228 no value 0.268259065
627 CYTOCHROME P450 4B1 (EC 1.14.14.1) (CYPIVB1) (P450-HP). [SWISSPROT;Acc:P13584] 0.0960386 0.358007 CYP4B1 0.268259001
628 SESTRIN 2 (HI95). [SWISSPROT;Acc:P58004] 0.553815 2.06448 SESN2 0.268258835
629 LIKELY ORTHOLOG OF RAT CYTOCHROME P450 4X1. [RefSeq;Acc:NM_178033] 0.0954996 0.355998 CYP4X1 0.26825881
630 CYTOCHROME P450 4F2 (EC 1.14.13.30) (CYPIVF2) (LEUKOTRIENE-B4 OMEGA- HYDROXYLASE) (LEUKOTRIENE-B4 20-MONOOXYGENASE) (CYTOCHROME P450- LTB-OMEGA). [SWISSPROT;Acc:P78329] 0.118945 0.443397 CYP4F2 0.268258468
631 CYTOCHROME P450 4F8 (EC 1.14.14.1) (CYPIVF8). [SWISSPROT;Acc:P98187] CYP4F8
632 CYTOCHROME P450 4A11 PRECURSOR (EC 1.14.15.3) (CYPIVA11) (FATTY ACID OMEGA-HYDROXYLASE) (P-450 HK OMEGA) (LAURIC ACID OMEGA-HYDROXYLASE) (CYP4AII) (P450-HL-OMEGA). [SWISSPROT;Acc:Q02928] CYP4A11
633 F-ACTIN CAPPING PROTEIN ALPHA-2 SUBUNIT (CAPZ ALPHA-2). [SWISSPROT;Acc:P47755] 0.121841 0.454193 no value 0.268258207
634 CYTOCHROME P450 4F12 (EC 1.14.14.1) (CYPIVF12). [SWISSPROT;Acc:Q9HCS2] 0.110995 0.413762 CYP4F12 0.268258081
635 SESTRIN 3. [SWISSPROT;Acc:P58005] 0.578823 2.15771 SESN3 0.268258014
636 "DJ18D14.4 (CYTOCHROME P450, SUBFAMILY IVA, POLYPEPTIDE 11). [SPTREMBL;Acc:Q9NTL5]" 0.116014 0.432472 CYP4A22 0.268257829
637 CYTOCHROME P450 4F3 (EC 1.14.13.30) (CYPIVF3) (LEUKOTRIENE-B4 OMEGA- HYDROXYLASE) (LEUKOTRIENE-B4 20-MONOOXYGENASE) (CYTOCHROME P450- LTB-OMEGA). [SWISSPROT;Acc:Q08477] 0.115475 0.430463 CYP4F3 0.268257667
638 "SPLICING FACTOR, ARGININE/SERINE-RICH 3 (PRE-MRNA SPLICING FACTOR SRP20) (X16 PROTEIN). [SWISSPROT;Acc:P23152]" 0.280063 1.04414 SFRS3 0.26822361
639 0.116093 0.432823 C18orf55 0.268222807
640 UPSTREAM BINDING PROTEIN 1 (LBP-1A). [RefSeq;Acc:NM_014517] 0.243481 0.907758 UBP1 0.268222368
641 LBP-9. [RefSeq;Acc:NM_014553] 0.198895 0.741531 TFCP2L1 0.268222097
642 "TRANSCRIPTION FACTOR CP2; TRANSCRIPTION FACTOR CP2, ALPHA GLOBIN. [RefSeq;Acc:NM_005653]" 0.209001 0.779209 TFCP2 0.268222005
643 UBIQUITIN-LIKE PROTEIN SMT3C PRECURSOR (UBIQUITIN-HOMOLOGY DOMAIN PROTEIN PIC1) (UBIQUITIN-LIKE PROTEIN UBL1) (UBIQUITIN-RELATED PROTEIN SUMO-1) (GAP MODIFYING PROTEIN 1) (GMP1) (SENTRIN). [SWISSPROT;Acc:Q93068] 0.473678 1.7666 SUMO1P3 0.268129741
644 0.0415188 0.154846 no value 0.268129626
645 UDP-GLUCOSE 6-DEHYDROGENASE (EC 1.1.1.22) (UDP-GLC DEHYDROGENASE) (UDP-GLCDH) (UDPGDH). [SWISSPROT;Acc:O60701] 0.124556 0.464538 UGDH 0.268128764
646 RAN-BINDING PROTEIN 2 (RANBP2) (NUCLEAR PORE COMPLEX PROTEIN NUP358) (NUCLEOPORIN NUP358) (358 KDA NUCLEOPORIN) (P270). [SWISSPROT;Acc:P49792] 0.464913 1.73399 RANBP2 0.268117463
647 RAN-BINDING PROTEIN 2-LIKE 1 ISOFORM 2; SPERM MEMBRANE PROTEIN BS-63; RAN-BINDING PROTEIN 2-LIKE 1. [RefSeq;Acc:NM_032260] 0.39546 1.47537 no value 0.268041237
648 0.365822 1.365 0.268001465
649 RETINOIC ACID INDUCED 17; PIAS-LIKE PROTEIN HZIMP10. [RefSeq;Acc:NM_020338] 0.204901 0.765015 ZMIZ1 0.267839193
650 C-JUN-AMINO-TERMINAL KINASE INTERACTING PROTEIN 3 (JNK-INTERACTING PROTEIN 3) (JIP-3) (JNK MAP KINASE SCAFFOLD PROTEIN 3) (MITOGEN- ACTIVATED PROTEIN KINASE 8-INTERACTING PROTEIN 3). [SWISSPROT;Acc:Q9UPT6] 0.218174 0.814576 MAPK8IP3 0.267837501

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/