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 final expected Hugo
Results: HTML CSV LaTeX Showing element 601 to 650 of 3206 in total
Rank
description
measured
final
expected
Hugo
601 0.0700114 0.269104872 0.260164 ZNF503
602 0.0897926 0.26910439 0.333672 ZNF703
603 ZINC FINGER PROTEIN ZIC 1 (ZINC FINGER PROTEIN OF THE CEREBELLUM 1). [SWISSPROT;Acc:Q15915] 0.272286 0.269091879 1.01187 ZIC1
604 HOMEOBOX PROTEIN OTX2. [SWISSPROT;Acc:P32243] 0.276018 0.26903388 1.02596 OTX2
605 HOMEOBOX PROTEIN OTX1. [SWISSPROT;Acc:P32242] 0.237139 0.269008429 0.88153 OTX1
606 CONE-ROD HOMEOBOX PROTEIN. [SWISSPROT;Acc:O43186] 0.226785 0.268999654 0.843068 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 0.26895292 0.29864 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 0.268952474 0.356373 LANCL2
609 HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE (EC 2.4.2.8) (HGPRT) (HGPRTASE). [SWISSPROT;Acc:P00492] 0.34395 0.268944163 1.27889 HPRT1
610 DJ947L8.1.6 (NOVEL CUB AND SUSHI (SCR REPEAT) DOMAIN PROTEIN) (FRAGMENT). [SPTREMBL;Acc:Q9H4W2] 0.0586244 0.268845272 0.21806 CSMD1
611 CALCIPRESSIN 1 (DOWN SYNDROME CRITICAL REGION PROTEIN 1) (MYOCYTE- ENRICHED CALCINEURIN INTERACTING PROTEIN 1) (MCIP1) (ADAPT78). [SWISSPROT;Acc:P53805] 0.346654 0.268844907 1.28942 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 0.268844667 1.04775 RCAN2
613 ZINC FINGER PROTEIN ZIC 4 (ZINC FINGER PROTEIN OF THE CEREBELLUM 4) (FRAGMENT). [SWISSPROT;Acc:Q8N9L1] 0.0906044 0.268844618 0.337014 ZIC4
614 DJ947L8.1.1 (NOVEL CUB AND SUSHI (SCR REPEAT) DOMAIN PROTEIN) (FRAGMENT). [SPTREMBL;Acc:Q9H4V7] 0.090945 0.26884454 0.338281 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 0.268844381 1.03901 RCAN3
616 P29ING4; CANDIDATE TUMOR SUPPRESSOR P33 ING1 HOMOLOG. [RefSeq;Acc:NM_016162] 0.0616259 0.268717978 0.229333 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 0.26856344 0.824699 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 0.268561278 0.865296 PPP3CB
619 P PROTEIN (MELANOCYTE-SPECIFIC TRANSPORTER PROTEIN). [SWISSPROT;Acc:Q04671] 0.116815 0.268558751 0.43497 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 0.268557151 1.05458 PPP3CA
621 F-ACTIN CAPPING PROTEIN ALPHA-1 SUBUNIT (CAPZ ALPHA-1). [SWISSPROT;Acc:P52907] 0.12721 0.268392514 0.47397 CAPZA1
622 SESTRIN 1 (P53-REGULATED PROTEIN PA26). [SWISSPROT;Acc:Q9Y6P5] 0.699473 0.268259411 2.60745 SESN1
623 CYTOCHROME P450 4F11 (EC 1.14.14.1) (CYPIVF11). [SWISSPROT;Acc:Q9HBI6] 0.113522 0.26825937 0.42318 CYP4F11
624 FLOTILLIN-1. [SWISSPROT;Acc:O75955] 0.11908 0.268259221 0.443899 FLOT1
625 0.102776 0.268259197 0.383122 CYP4F22
626 0.0869771 0.268259065 0.324228 no value
627 CYTOCHROME P450 4B1 (EC 1.14.14.1) (CYPIVB1) (P450-HP). [SWISSPROT;Acc:P13584] 0.0960386 0.268259001 0.358007 CYP4B1
628 SESTRIN 2 (HI95). [SWISSPROT;Acc:P58004] 0.553815 0.268258835 2.06448 SESN2
629 LIKELY ORTHOLOG OF RAT CYTOCHROME P450 4X1. [RefSeq;Acc:NM_178033] 0.0954996 0.26825881 0.355998 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 0.268258468 0.443397 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 0.268258207 0.454193 no value
634 CYTOCHROME P450 4F12 (EC 1.14.14.1) (CYPIVF12). [SWISSPROT;Acc:Q9HCS2] 0.110995 0.268258081 0.413762 CYP4F12
635 SESTRIN 3. [SWISSPROT;Acc:P58005] 0.578823 0.268258014 2.15771 SESN3
636 "DJ18D14.4 (CYTOCHROME P450, SUBFAMILY IVA, POLYPEPTIDE 11). [SPTREMBL;Acc:Q9NTL5]" 0.116014 0.268257829 0.432472 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 0.268257667 0.430463 CYP4F3
638 "SPLICING FACTOR, ARGININE/SERINE-RICH 3 (PRE-MRNA SPLICING FACTOR SRP20) (X16 PROTEIN). [SWISSPROT;Acc:P23152]" 0.280063 0.26822361 1.04414 SFRS3
639 0.116093 0.268222807 0.432823 C18orf55
640 UPSTREAM BINDING PROTEIN 1 (LBP-1A). [RefSeq;Acc:NM_014517] 0.243481 0.268222368 0.907758 UBP1
641 LBP-9. [RefSeq;Acc:NM_014553] 0.198895 0.268222097 0.741531 TFCP2L1
642 "TRANSCRIPTION FACTOR CP2; TRANSCRIPTION FACTOR CP2, ALPHA GLOBIN. [RefSeq;Acc:NM_005653]" 0.209001 0.268222005 0.779209 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 0.268129741 1.7666 SUMO1P3
644 0.0415188 0.268129626 0.154846 no value
645 UDP-GLUCOSE 6-DEHYDROGENASE (EC 1.1.1.22) (UDP-GLC DEHYDROGENASE) (UDP-GLCDH) (UDPGDH). [SWISSPROT;Acc:O60701] 0.124556 0.268128764 0.464538 UGDH
646 RAN-BINDING PROTEIN 2 (RANBP2) (NUCLEAR PORE COMPLEX PROTEIN NUP358) (NUCLEOPORIN NUP358) (358 KDA NUCLEOPORIN) (P270). [SWISSPROT;Acc:P49792] 0.464913 0.268117463 1.73399 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 0.268041237 1.47537 no value
648 0.365822 0.268001465 1.365
649 RETINOIC ACID INDUCED 17; PIAS-LIKE PROTEIN HZIMP10. [RefSeq;Acc:NM_020338] 0.204901 0.267839193 0.765015 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 0.267837501 0.814576 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/