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 final Hugo
Results: HTML CSV LaTeX Showing element 601 to 650 of 3206 in total
Rank
description
measured
expected
final
Hugo
601 0.0700114 0.260164 0.269104872 ZNF503
602 0.0897926 0.333672 0.26910439 ZNF703
603 ZINC FINGER PROTEIN ZIC 1 (ZINC FINGER PROTEIN OF THE CEREBELLUM 1). [SWISSPROT;Acc:Q15915] 0.272286 1.01187 0.269091879 ZIC1
604 HOMEOBOX PROTEIN OTX2. [SWISSPROT;Acc:P32243] 0.276018 1.02596 0.26903388 OTX2
605 HOMEOBOX PROTEIN OTX1. [SWISSPROT;Acc:P32242] 0.237139 0.88153 0.269008429 OTX1
606 CONE-ROD HOMEOBOX PROTEIN. [SWISSPROT;Acc:O43186] 0.226785 0.843068 0.268999654 CRX
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 0.26895292 LANCL1
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 0.268952474 LANCL2
609 HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE (EC 2.4.2.8) (HGPRT) (HGPRTASE). [SWISSPROT;Acc:P00492] 0.34395 1.27889 0.268944163 HPRT1
610 DJ947L8.1.6 (NOVEL CUB AND SUSHI (SCR REPEAT) DOMAIN PROTEIN) (FRAGMENT). [SPTREMBL;Acc:Q9H4W2] 0.0586244 0.21806 0.268845272 CSMD1
611 CALCIPRESSIN 1 (DOWN SYNDROME CRITICAL REGION PROTEIN 1) (MYOCYTE- ENRICHED CALCINEURIN INTERACTING PROTEIN 1) (MCIP1) (ADAPT78). [SWISSPROT;Acc:P53805] 0.346654 1.28942 0.268844907 RCAN1
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 0.268844667 RCAN2
613 ZINC FINGER PROTEIN ZIC 4 (ZINC FINGER PROTEIN OF THE CEREBELLUM 4) (FRAGMENT). [SWISSPROT;Acc:Q8N9L1] 0.0906044 0.337014 0.268844618 ZIC4
614 DJ947L8.1.1 (NOVEL CUB AND SUSHI (SCR REPEAT) DOMAIN PROTEIN) (FRAGMENT). [SPTREMBL;Acc:Q9H4V7] 0.090945 0.338281 0.26884454 no value
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 0.268844381 RCAN3
616 P29ING4; CANDIDATE TUMOR SUPPRESSOR P33 ING1 HOMOLOG. [RefSeq;Acc:NM_016162] 0.0616259 0.229333 0.268717978 ING4
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 0.26856344 PPP3CC
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 0.268561278 PPP3CB
619 P PROTEIN (MELANOCYTE-SPECIFIC TRANSPORTER PROTEIN). [SWISSPROT;Acc:Q04671] 0.116815 0.43497 0.268558751 OCA2
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 0.268557151 PPP3CA
621 F-ACTIN CAPPING PROTEIN ALPHA-1 SUBUNIT (CAPZ ALPHA-1). [SWISSPROT;Acc:P52907] 0.12721 0.47397 0.268392514 CAPZA1
622 SESTRIN 1 (P53-REGULATED PROTEIN PA26). [SWISSPROT;Acc:Q9Y6P5] 0.699473 2.60745 0.268259411 SESN1
623 CYTOCHROME P450 4F11 (EC 1.14.14.1) (CYPIVF11). [SWISSPROT;Acc:Q9HBI6] 0.113522 0.42318 0.26825937 CYP4F11
624 FLOTILLIN-1. [SWISSPROT;Acc:O75955] 0.11908 0.443899 0.268259221 FLOT1
625 0.102776 0.383122 0.268259197 CYP4F22
626 0.0869771 0.324228 0.268259065 no value
627 CYTOCHROME P450 4B1 (EC 1.14.14.1) (CYPIVB1) (P450-HP). [SWISSPROT;Acc:P13584] 0.0960386 0.358007 0.268259001 CYP4B1
628 SESTRIN 2 (HI95). [SWISSPROT;Acc:P58004] 0.553815 2.06448 0.268258835 SESN2
629 LIKELY ORTHOLOG OF RAT CYTOCHROME P450 4X1. [RefSeq;Acc:NM_178033] 0.0954996 0.355998 0.26825881 CYP4X1
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 0.268258468 CYP4F2
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 0.268258207 no value
634 CYTOCHROME P450 4F12 (EC 1.14.14.1) (CYPIVF12). [SWISSPROT;Acc:Q9HCS2] 0.110995 0.413762 0.268258081 CYP4F12
635 SESTRIN 3. [SWISSPROT;Acc:P58005] 0.578823 2.15771 0.268258014 SESN3
636 "DJ18D14.4 (CYTOCHROME P450, SUBFAMILY IVA, POLYPEPTIDE 11). [SPTREMBL;Acc:Q9NTL5]" 0.116014 0.432472 0.268257829 CYP4A22
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 0.268257667 CYP4F3
638 "SPLICING FACTOR, ARGININE/SERINE-RICH 3 (PRE-MRNA SPLICING FACTOR SRP20) (X16 PROTEIN). [SWISSPROT;Acc:P23152]" 0.280063 1.04414 0.26822361 SFRS3
639 0.116093 0.432823 0.268222807 C18orf55
640 UPSTREAM BINDING PROTEIN 1 (LBP-1A). [RefSeq;Acc:NM_014517] 0.243481 0.907758 0.268222368 UBP1
641 LBP-9. [RefSeq;Acc:NM_014553] 0.198895 0.741531 0.268222097 TFCP2L1
642 "TRANSCRIPTION FACTOR CP2; TRANSCRIPTION FACTOR CP2, ALPHA GLOBIN. [RefSeq;Acc:NM_005653]" 0.209001 0.779209 0.268222005 TFCP2
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 0.268129741 SUMO1P3
644 0.0415188 0.154846 0.268129626 no value
645 UDP-GLUCOSE 6-DEHYDROGENASE (EC 1.1.1.22) (UDP-GLC DEHYDROGENASE) (UDP-GLCDH) (UDPGDH). [SWISSPROT;Acc:O60701] 0.124556 0.464538 0.268128764 UGDH
646 RAN-BINDING PROTEIN 2 (RANBP2) (NUCLEAR PORE COMPLEX PROTEIN NUP358) (NUCLEOPORIN NUP358) (358 KDA NUCLEOPORIN) (P270). [SWISSPROT;Acc:P49792] 0.464913 1.73399 0.268117463 RANBP2
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 0.268041237 no value
648 0.365822 1.365 0.268001465
649 RETINOIC ACID INDUCED 17; PIAS-LIKE PROTEIN HZIMP10. [RefSeq;Acc:NM_020338] 0.204901 0.765015 0.267839193 ZMIZ1
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 0.267837501 MAPK8IP3

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/