- -
实验二Ensemble 使用
1.1在Ensemble页面All genomes的下拉菜单中选择human,查看这个物种的具体信息,人的染色体和基因数量如图所示,基因数量主要看Alternative sequence的图示。genetic variation有Short Variants (329,179,721)和Structural variants (5,955,877)。
1.2 在 Ensemble 首页进行human for MAPK4搜索,在结果页面追加Restrict category to 为gene,筛选到117条序列,打开登录号为ENSG的目标序列,查看Gene-based displays。
- 考试资料
- -
1.2.1这个基因有6个可变剪接,他们之间序列长度不同,其中4个可以编码蛋白,所编码蛋白的氨基酸数量也不同。
1.2.2 在Comparative Genomics项Genomic alignments中,选择multiple,然后选择27种amniota vertebrates Pecan进行比对,在configure this page中勾选Show conservation regions,在Alignments (text)部分,可以看到蓝色高亮显示的保守区域了。
1.2.3 MAPK4基因位于Chromosome 18: 50,560,078-50,731,824。有10个外显子,9内含子。从sequence项可以看到core exons的数量,从基因结构图示也可以看到内含子和外显子的数量。
1.2.4 MAPK4 属于PTHR24055_SF25(2 genes)蛋白家族。家族其他成员还有MAPK4-001,MAPK4-002,MAPK4-003,MAPK4-005。
1.2.5从GO注释中,我们了解到MAPK4基因可编码蛋白的四个转录本,分别在分子功能、生物学进程和细胞组分方面的信息。
- 考试资料
- -
1.2.6这个基因的Structural variants的genetic variation有SNP、deletion、insertion、CNV(拷贝数变异)和short tandem repeat variation。
1.2.7在gene expression项,可以看到 32 experiments中MAPK基因的表达情况,下载Table content,为TSV文件,用Excel表打开查看具体表达情况。可知MAPK4在人体的144个组织(附下载文件)中不同程度的表达,这些组织分别为: cerebellum spinal cord diencephalon midbrain hindbrain gland
forebrain
basal ganglion
brain fragmentadrenal
cerebral lung caudate
temporal lobemedulla oblongata
heart
kidney testis ovary
cortex choroid plexus telencephalon nucleus bronchus
locus ceruleus
cervix, uterine
heart muscle nasopharynx parathyroid gland
nucleus accumbens umbilical cord diencephalon and midbrain
- 考试资料
- -
oral mucosa telencephalic ventricle globus pallidus muscle of arm prefrontal
cortex putamen pons
brain eyehindbrain without cerebellum frontal lobe
esophagus pituitary and diencephalon cerebellar hemisphere right renal cortexright renal pelvis hippocampus rectum left kidney left renal cortex renal pelvishippocampal formation
endometrium
saliva-secreting gland tonsil
thyroid
gland Brodmann (1909) area 9 duodenum left renal pelvis forebrain fragment
dorsal thalamus Brodmann (1909) area 24 skeletal muscle of trunk hindbrain
small intestine
occipital lobe brain meninx hypothalamus throat thymusplacenta adipose tissue
prostate gland
amygdala
fragment
forebrain and midbrain
gall bladder parietal lobe smooth muscle tissue trachea muscle of leg colonseminal vesicle liver fallopian tube urinary bladder skeletal muscle tissuediaphragm large intestine sigmoid colon epididymis lymph node olfactory apparatus substantia nigra
tibial artery stomach
hippocampus proper
atrium auricular region
C1
vermiform appendix cortex of kidney occipital cortex
zone of skin bone marrow middle frontal gyrus middle temporal gyrus
segment of cervical spinal cord pancreas breast spleen vagina coronary artery
pituitary gland
heart left ventricle mitral valve vas deferens esophagogastric
junction tongue esophagus muscularis mucosa pineal body pulmonary valve aorta
tibial nerve uterus ectocervix
endocervix transverse colon left cardiac minor salivary gland suprapubic skin dura
atrium tricuspid valve lower leg skin
mater esophagus mucosa subcutaneous adipose tissue artery parotid gland penis
small intestine Peyer's patch uterine cervix submandibular gland soft tissue
- 考试资料
- -
leukocyte EBV-transformed lymphocyte blood greater omentumtransformed
skin fibroblast
1.2.8在regulation项中的图示中,我们可以看到regulatory build,分析基因的motif
feature,enhancer,promotor和transcription factor binding site。且图示下方有各调控区域的功能,序列,序列长度和精确位点。
1.2.9下载你研究的生物分子的 rtf 格式的序列文件,用 word 打开浏览。附下载文件及部分序列。
- 考试资料
生物信息学实验指导实验二ensemble使用 - 图文
![](/skin/haowen/images/icon_star.png)
![](/skin/haowen/images/icon_star.png)
![](/skin/haowen/images/icon_star.png)
![](/skin/haowen/images/icon_star.png)