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At a glimpse. In each package will be used for specific type of analysis. For my case, I am interested in the data from GeoDataset which in the gene expression data deposited on NCBI. Also the ggplot that can represent data in the graphical ways. One thing that I notice about myself is that I totally forget some functions/definitions in mathematics, I have not used some definitions for a while ago and got shocked during the training. Some definitions are used for turning some values to make the calculation go through the pipeline, for example, complex number. It will be a steep learning curve for sure, the commands will be new to me but the pipeline or thinking-step to get the output should be the same and can be applied to any computer programming. PS. I have provided information for the self-study in the useful links --- Additional - before I forget, each window in R has a different function (pic below); Window 1\\ script writing-> use for writing the scri...

Ubiquitin chain diversity at a glance (doi: 10.1242/jcs.183954) Human Ub (76 amino acids)--> 7 Lys ·         MQIFV K TLTG K TITLEVEPSDTIENV K A K IQD K EGIPPDQQRLIFAG K QLEDGRTLSDYNIQ K ESTLHLVLRLRGG Since I have worked with E3 ubiquitin ligase, I need to read and recall a lot on the ubiquitin. The last time that I could recall from molecular biology was that the ubiquitination was for the protein degradation. Nowadays, with the advantage of the technology, they are not meant to function only as proteasomal degradation, besides, it involves diverse kinds of functions, for example, endocytosis, DNA repair and subcellular localization. Things are even more complicated when it is found out that ubiquitin can be subjected to modifications, phosphorylation (Ub-P) and acetylation (Ub-Ac)!! I have not kept track on this yet. but I will try to update how it relates to the cellular process and also whether it causes the disease. Ubiquit...

Skimming: A comprehensive framework of E2-RING E3 interactions of the human ubiquitin-proteasome system (doi: 10.1038/msb.2009.55) Using yeast two-hybrid (Y2H) screening for the interaction partner between E2-E3 and vice versa Reporter system: LacZ LEU2 Human cDNA-->produce only the domain (partial) E2 -- UBC-fold (highly conserved) E3 -- RING-finger catalytic domain (interact with E2 through the UBC fold) E2 interacts more than one E3 and vice versa size of circles reflects the numbers of interaction partners of either E2 (red) or E3 (blue). Environment to examine the interaction in yeast without any stimulant Platform of yeast two-hybrid screening Each domain connected to reporter protein at the C-terminal//each transform to yeast (haploid stage)//mating between two different sexual strain. If there is the interaction between E2-E3-->yeast can grow on the selective media.

Note: LIG4 mediates Wnt signaling-induced radioresistance (doi: 10.1038/ncomms10994) This work is very nice piece and easy to follow step by step to test their hypothesis. Focus tumor: CRC Cell line used (endogenous environment): SW620 HCT116 HT15 COLO205 HCC2998 KM12 Cellular event marker: g-H2Ax --> DNA double-strand break Reporter for wnt-acivity: 7TGP Reporter for functional stem cell (using the genetic engineered approach): telomerase reverse transcriptase ( TERT ) --> expressed only in self-renewing cells Inhibitor: iCRT14 -- break the interaction between b-catenin-TCF--> no transcription occur (less LIG4) SCR7 -- break the interaction between LIG4-DNA-->no DNA repair by LIG4 b-catenin targeted genes (transcript product): CD44 CD133 Axin2 Wnt is related to radioresistant but the underly mechanism is unk --> therefore, this study want to investigate. How it links to DNA repair? --> Wnt regulates the stemness and thi...

The E3 ligase RNF43 inhibits Wnt signaling downstream of mutated beta-catenin by sequestering TCF4 to the nuclear membrane (doi: 10.1126/scisignal.aac6757) 1.Abnormal in wnt signaling -- >90% of sporadic colon tumors 2.Mutation mostly found -- APC (adenomatous polyposis coli) or b-catenin 3.Activation of Fz causes degradation complex releases b-catenin --> b-catenin localize to nucleus 4.b-catenin bind to TCF-4 (transcription factor) --> activate the transcription corresponding to this TF 5.RNF43 involves with DNA-damage response This paper points out three key previous findings; 1.RNF43 is tumor suppressor by reducing the abundance of Fz at plasma mb, thereby, reducing the wnt signaling. 2.Conversely, RNF43 is found at the nucleus envelope, ER and nucleoplasm --> but related to the evidence showing that RNF43 is related to DNA damage response. 3.RNF43 oncogene? or RNF43 tumor suppressor? --> numbers of research, lately, showed it might be tumo...

Note for myself on: Tumour-associated mutations of PA-TM-RING ubiquitin ligases RNF167/RNF13 identify the PA domain as a determinant for endosomal localization (doi: 10.1042/BJ20131067) 1. Investigate the function of RNF167/RNF13 at the cellular level  -- PA domain in these two proteins were shown to function as endosomal recycling processes -- using the information from a functional study in fruitfly (homolog) and apply to the human cell 2. Using the information from COSMID to identify the mutations that could contribute to the cancer 3. Identified those mutations in human cell line// there are two separate sets; -- PA domain function --> endosomal localization -- RING domain function --> E3 ubiquitin ligase It works independently but coordinatingly to get the correct function within the cell --> right place and right time to function. Cell line; Using HEK-293 to study the function Antibodies; FK2 (recognize K29-, K48-, K63-linked poly ubiquitin...