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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Gene Rank measured description expected Hugo final
Results: HTML CSV LaTeX Showing element 608 to 657 of 3206 in total
Rank
measured
description
expected
Hugo
final
608 0.0958474 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] 0.356373 LANCL2 0.268952474
609 0.34395 HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE (EC 2.4.2.8) (HGPRT) (HGPRTASE). [SWISSPROT;Acc:P00492] 1.27889 HPRT1 0.268944163
610 0.0586244 DJ947L8.1.6 (NOVEL CUB AND SUSHI (SCR REPEAT) DOMAIN PROTEIN) (FRAGMENT). [SPTREMBL;Acc:Q9H4W2] 0.21806 CSMD1 0.268845272
611 0.346654 CALCIPRESSIN 1 (DOWN SYNDROME CRITICAL REGION PROTEIN 1) (MYOCYTE- ENRICHED CALCINEURIN INTERACTING PROTEIN 1) (MCIP1) (ADAPT78). [SWISSPROT;Acc:P53805] 1.28942 RCAN1 0.268844907
612 0.281682 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] 1.04775 RCAN2 0.268844667
613 0.0906044 ZINC FINGER PROTEIN ZIC 4 (ZINC FINGER PROTEIN OF THE CEREBELLUM 4) (FRAGMENT). [SWISSPROT;Acc:Q8N9L1] 0.337014 ZIC4 0.268844618
614 0.090945 DJ947L8.1.1 (NOVEL CUB AND SUSHI (SCR REPEAT) DOMAIN PROTEIN) (FRAGMENT). [SPTREMBL;Acc:Q9H4V7] 0.338281 no value 0.26884454
615 0.279332 CALCIPRESSIN 3 (DOWN SYNDROME CANDIDATE REGION 1-LIKE PROTEIN 2) (MYOCYTE-ENRICHED CALCINEURIN INTERACTING PROTEIN 3) (MCIP3). [SWISSPROT;Acc:Q9UKA8] 1.03901 RCAN3 0.268844381
616 0.0616259 P29ING4; CANDIDATE TUMOR SUPPRESSOR P33 ING1 HOMOLOG. [RefSeq;Acc:NM_016162] 0.229333 ING4 0.268717978
617 0.221484 "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]" 0.824699 PPP3CC 0.26856344
618 0.232385 "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]" 0.865296 PPP3CB 0.268561278
619 0.116815 P PROTEIN (MELANOCYTE-SPECIFIC TRANSPORTER PROTEIN). [SWISSPROT;Acc:Q04671] 0.43497 OCA2 0.268558751
620 0.283215 "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]" 1.05458 PPP3CA 0.268557151
621 0.12721 F-ACTIN CAPPING PROTEIN ALPHA-1 SUBUNIT (CAPZ ALPHA-1). [SWISSPROT;Acc:P52907] 0.47397 CAPZA1 0.268392514
622 0.699473 SESTRIN 1 (P53-REGULATED PROTEIN PA26). [SWISSPROT;Acc:Q9Y6P5] 2.60745 SESN1 0.268259411
623 0.113522 CYTOCHROME P450 4F11 (EC 1.14.14.1) (CYPIVF11). [SWISSPROT;Acc:Q9HBI6] 0.42318 CYP4F11 0.26825937
624 0.11908 FLOTILLIN-1. [SWISSPROT;Acc:O75955] 0.443899 FLOT1 0.268259221
625 0.102776 0.383122 CYP4F22 0.268259197
626 0.0869771 0.324228 no value 0.268259065
627 0.0960386 CYTOCHROME P450 4B1 (EC 1.14.14.1) (CYPIVB1) (P450-HP). [SWISSPROT;Acc:P13584] 0.358007 CYP4B1 0.268259001
628 0.553815 SESTRIN 2 (HI95). [SWISSPROT;Acc:P58004] 2.06448 SESN2 0.268258835
629 0.0954996 LIKELY ORTHOLOG OF RAT CYTOCHROME P450 4X1. [RefSeq;Acc:NM_178033] 0.355998 CYP4X1 0.26825881
630 0.118945 CYTOCHROME P450 4F2 (EC 1.14.13.30) (CYPIVF2) (LEUKOTRIENE-B4 OMEGA- HYDROXYLASE) (LEUKOTRIENE-B4 20-MONOOXYGENASE) (CYTOCHROME P450- LTB-OMEGA). [SWISSPROT;Acc:P78329] 0.443397 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 0.121841 F-ACTIN CAPPING PROTEIN ALPHA-2 SUBUNIT (CAPZ ALPHA-2). [SWISSPROT;Acc:P47755] 0.454193 no value 0.268258207
634 0.110995 CYTOCHROME P450 4F12 (EC 1.14.14.1) (CYPIVF12). [SWISSPROT;Acc:Q9HCS2] 0.413762 CYP4F12 0.268258081
635 0.578823 SESTRIN 3. [SWISSPROT;Acc:P58005] 2.15771 SESN3 0.268258014
636 0.116014 "DJ18D14.4 (CYTOCHROME P450, SUBFAMILY IVA, POLYPEPTIDE 11). [SPTREMBL;Acc:Q9NTL5]" 0.432472 CYP4A22 0.268257829
637 0.115475 CYTOCHROME P450 4F3 (EC 1.14.13.30) (CYPIVF3) (LEUKOTRIENE-B4 OMEGA- HYDROXYLASE) (LEUKOTRIENE-B4 20-MONOOXYGENASE) (CYTOCHROME P450- LTB-OMEGA). [SWISSPROT;Acc:Q08477] 0.430463 CYP4F3 0.268257667
638 0.280063 "SPLICING FACTOR, ARGININE/SERINE-RICH 3 (PRE-MRNA SPLICING FACTOR SRP20) (X16 PROTEIN). [SWISSPROT;Acc:P23152]" 1.04414 SFRS3 0.26822361
639 0.116093 0.432823 C18orf55 0.268222807
640 0.243481 UPSTREAM BINDING PROTEIN 1 (LBP-1A). [RefSeq;Acc:NM_014517] 0.907758 UBP1 0.268222368
641 0.198895 LBP-9. [RefSeq;Acc:NM_014553] 0.741531 TFCP2L1 0.268222097
642 0.209001 "TRANSCRIPTION FACTOR CP2; TRANSCRIPTION FACTOR CP2, ALPHA GLOBIN. [RefSeq;Acc:NM_005653]" 0.779209 TFCP2 0.268222005
643 0.473678 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] 1.7666 SUMO1P3 0.268129741
644 0.0415188 0.154846 no value 0.268129626
645 0.124556 UDP-GLUCOSE 6-DEHYDROGENASE (EC 1.1.1.22) (UDP-GLC DEHYDROGENASE) (UDP-GLCDH) (UDPGDH). [SWISSPROT;Acc:O60701] 0.464538 UGDH 0.268128764
646 0.464913 RAN-BINDING PROTEIN 2 (RANBP2) (NUCLEAR PORE COMPLEX PROTEIN NUP358) (NUCLEOPORIN NUP358) (358 KDA NUCLEOPORIN) (P270). [SWISSPROT;Acc:P49792] 1.73399 RANBP2 0.268117463
647 0.39546 RAN-BINDING PROTEIN 2-LIKE 1 ISOFORM 2; SPERM MEMBRANE PROTEIN BS-63; RAN-BINDING PROTEIN 2-LIKE 1. [RefSeq;Acc:NM_032260] 1.47537 no value 0.268041237
648 0.365822 1.365 0.268001465
649 0.204901 RETINOIC ACID INDUCED 17; PIAS-LIKE PROTEIN HZIMP10. [RefSeq;Acc:NM_020338] 0.765015 ZMIZ1 0.267839193
650 0.218174 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] 0.814576 MAPK8IP3 0.267837501
651 0.0774957 DAZ ASSOCIATED PROTEIN 1 ISOFORM B; DELETED IN AZOOSPERMIA ASSOCIATED PROTEIN 1. [RefSeq;Acc:NM_018959] 0.289339 DAZAP1 0.267837035
652 0.170567 0.63684 ZMIZ2 0.267833365
653 0.40611 AUTOPHAGY PROTEIN 5-LIKE (APG5-LIKE) (APOPTOSIS-SPECIFIC PROTEIN). [SWISSPROT;Acc:Q9H1Y0] 1.51635 ATG5 0.267820754
654 0.113218 CYSTEINE-RICH PROTEIN 1 (CYSTEINE-RICH INTESTINAL PROTEIN) (CRIP) (CYSTEINE-RICH HEART PROTEIN) (HCRHP). [SWISSPROT;Acc:P50238] 0.423045 no value 0.267626375
655 0.173445 EUKARYOTIC TRANSLATION INITIATION FACTOR 4E (EIF-4E) (EIF4E) (MRNA CAP-BINDING PROTEIN) (EIF-4F 25 KDA SUBUNIT). [SWISSPROT;Acc:P06730] 0.648176 EIF4E 0.267589358
656 0.0241104 BAI1-ASSOCIATED PROTEIN 3; BAI-ASSOCIATED PROTEIN 3. [RefSeq;Acc:NM_003933] 0.0901025 BAIAP3 0.26758858
657 0.0404532 STEP II SPLICING FACTOR SLU7. [RefSeq;Acc:NM_006425] 0.151367 SLU7 0.267252439

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/