生物信息學(xué)實(shí)驗(yàn)指導(dǎo) 實(shí)驗(yàn)二 Ensemble 使用

1、實(shí)驗(yàn)二Ensemble 使用1.1在Ensemble頁面All genomes的下拉菜單中選擇human，查看這個(gè)物種的具體信息，人的染色體和基因數(shù)量如圖所示，基因數(shù)量主要看Alternative sequence的圖示。genetic variation有Short Variants （329,179,721）和Structural variants （5,955,877）。1.2 在 Ensemble 首頁進(jìn)行human for MAPK4搜索，在結(jié)果頁面追加Restrict category to 為gene，篩選到117條序列，打開登錄號為ENSG00000141639的目標(biāo)序列，查看

2、Gene-based displays。1.2.1這個(gè)基因有6個(gè)可變剪接，他們之間序列長度不同，其中4個(gè)可以編碼蛋白，所編碼蛋白的氨基酸數(shù)量也不同。1.2.2 在 HYPERLINK /Homo_sapiens/Gene/Compara?align=1087;db=core;g=ENSG00000141639;r=18:50560078-50731824 o Comparative Genomics Comparative Genomics項(xiàng) HYPERLINK /Homo_sapiens/Gene/Compara_Alignments?align=1087;db=core;g=ENSG000

3、00141639;r=18:50560078-50731824 o Genomic alignments Genomic alignments中，選擇multiple，然后選擇27種amniota vertebrates Pecan進(jìn)行比對，在configure this page中勾選Show conservation regions，在 HYPERLINK /Help/View?id=202 Alignments (text)部分，可以看到藍(lán)色高亮顯示的保守區(qū)域了。1.2.3 MAPK4基因位于 HYPERLINK /Homo_sapiens/Location/View?db=core;g

4、=ENSG00000141639;r=18:50560078-50731824 Chromosome 18: 50,560,078-50,731,824。有10個(gè)外顯子，9內(nèi)含子。從sequence項(xiàng)可以看到core exons的數(shù)量，從基因結(jié)構(gòu)圖示也可以看到內(nèi)含子和外顯子的數(shù)量。1.2.4 MAPK4 屬于 HYPERLINK /Multi/Family/Details?fm=PTHR24055_SF25 PTHR24055_SF25( HYPERLINK /Homo_sapiens/Gene/Family/Genes?cdb=compara;db=core;family=PTHR24055

5、_SF25;g=ENSG00000141639;r=18:48018125-48189873;t=ENST00000400384 2 genes)蛋白家族。家族其他成員還有MAPK4-001，MAPK4-002，MAPK4-003，MAPK4-005。1.2.5從GO注釋中，我們了解到MAPK4基因可編碼蛋白的四個(gè)轉(zhuǎn)錄本，分別在分子功能、生物學(xué)進(jìn)程和細(xì)胞組分方面的信息。1.26這個(gè)基因的 HYPERLINK /Homo_sapiens/Gene/StructuralVariation_Gene?db=core;g=ENSG00000141639;r=18:48018125-48189873;t

6、=ENST00000400384 l sv_table Structural variants的genetic variation有SNP、deletion、insertion、CNV（拷貝數(shù)變異）和short tandem repeat variation。1.2.7在gene expression項(xiàng)，可以看到32 experiments中MAPK基因的表達(dá)情況，下載Table content，為TSV文件，用Excel表打開查看具體表達(dá)情況?？芍狹APK4在人體的144個(gè)組織（附下載文件）中不同程度的表達(dá)，這些組織分別為：cerebellumspinal corddiencephalonm

7、idbrainhindbrainbrain fragmentadrenal glandforebrainbasal gangliontemporal lobemedulla oblongatacerebral cortexchoroid plexustelencephalonheartkidney testisovarylungcaudate nucleusbronchuscervix, uterineheart musclenasopharynxparathyroid glandlocus ceruleusnucleus accumbens umbilical corddiencephalo

8、n and midbrainoral mucosatelencephalic ventricle globus pallidusmuscle of armprefrontal cortexputamenponsbrain eyehindbrain without cerebellumfrontal lobeesophaguspituitary and diencephaloncerebellar hemisphereright renal cortexright renal pelvis hippocampusrectumleft kidneyleft renal cortexrenal pe

9、lvishippocampal formationendometriumsaliva-secreting glandtonsilthyroid gland Brodmann (1909) area 9duodenumleft renal pelvisforebrain fragmentdorsal thalamus Brodmann (1909) area 24skeletal muscle of trunkhindbrain fragmentsmall intestineoccipital lobebrain meninxhypothalamus throatthymusforebrain

10、and midbrainplacentaadipose tissueprostate glandamygdalagall bladder parietal lobesmooth muscle tissue trachea muscle of legcolonseminal vesicle liver fallopian tubeurinary bladderskeletal muscle tissuediaphragmlarge intestine sigmoid colon epididymistibial arterystomachlymph nodeolfactory apparatus

11、 substantia nigrahippocampus propervermiform appendixcortex of kidney occipital cortexatrium auricular regionzone of skinbone marrowmiddle frontal gyrusmiddle temporal gyrusC1 segment of cervical spinal cord pancreas breastspleenvaginacoronary arterypituitary glandheart left ventricle mitral valveva

12、s deferensesophagogastric junctiontongue esophagus muscularis mucosa pineal bodypulmonary valveaortatibial nerveuterusectocervixendocervix transverse colonleft cardiac atrium tricuspid valvelower leg skinminor salivary glandsuprapubic skindura materesophagus mucosasubcutaneous adipose tissuearterypa

13、rotid gland penissmall intestine Peyers patchuterine cervix submandibular gland soft tissueleukocyteEBV-transformed lymphocyteblood greater omentumtransformed skin fibroblast 1.2.8在regulation項(xiàng)中的圖示中，我們可以看到regulatory build，分析基因的motif feature,enhancer,promotor和transcription factor binding site。且圖示下方有各調(diào)

14、控區(qū)域的功能，序列，序列長度和精確位點(diǎn)。1.2.9下載你研究的生物分子的 rtf 格式的序列文件，用 word 打開瀏覽。附下載文件及部分序列。50559478 CGGAATCCCAGGCCGGCTGGGGACCGGTGCACTTGGGCTCCGCGCCCCCTCGACCCTCGG 5055953750559538 CCCAGTGCCCCTTCCCGCGCGCGCGGGTCTCCCCGGTTCCAGAGCCCACCGGTCCCCGCC 5055959750559598 GGCTCCTTCTCCCCACCCACCCTCCCACCGGGCCCCCGGCGGCTGCAGCCGCGCGGGGCT 50

15、55965750559658 GGCGGGGCGGCGACCGGGCTCAGGCAGATCCCCGCTTCCCGCCTTCTCGGCGCCCCCTCC 5055971750559718 CTCCCGGACGGAGCCCGAGGATCCCCCACCCACGGCGGGCGTGAGGAAGGGCTTCTGAGT 5055977750559778 GACTGGAGCTCTACCGCGTGTGCCCCGGGAAGGCCAGGCTACCCGGGACGGGGCTCGGCT 5055983750559838 CCCCAGGTGAGCTCGTCTCCGCGGGACTGGGTCCGGGAAGGCCCCAGGACC

16、GCGCGGCTG 5055989750559898 AGCGGCCTGGAGGCTGCGGGAGGGCAGAGCAGGGCGCGCGGGAGACTGCCGCCCCCGGGC 5055995750559958 GCCCAGGGCCCGGCTCCCCAGCGCCACCGCCGCAGCAGGTGGGGGCCCAGTGGGCGGGGG 5056001750560018 CGGGGCCCGGCTCTGGGCGGAGCCGAGGCGGCGGCGGCGCAGGCTGGGGCCGGGGCCGGG 5056007750560078 GCGGGAGCCGGAGCCCGAGCTGGAGCAGCGAGCCGGGCT

17、GTCGGGGCGACCGCGGGAGCT 5056013750560138 CGCCGTGCGCCGTGGCTGGGACCGGCCTGGCCGAGCGCGCCGGCGCCGCGGCCGCAGACA 5056019750560198 AAGGGCGGCTCGCGCCCGGGCCGCCACGCTCTCGGGCTCTGCCTCGGTAAGTGGCTCCCC 5056025750560258 TCCGCTGGCTTTCTCCTCCCGCCGCCTGCGCCTCTCGGAGTTCGGCGGGCTCCGGAGAAG 5056031750560318 CGGGGAAGAGATGAGACTTCCCCGCCC

18、GCACTGCCTCCCCACCTTACCCTAACAATAAGC 5056037750560378 CCCCCAGGCCAAGCCACTGCCAAACTAGCGAGTTTCCGAGCGGCGGGGGTCTCCCGCGGG 5056043750560438 ACCCGCCCGGCTGCCCTGGGTGAGCTCCTCGCCTGCAGACCGCGCGCCGGTGCTGTCCTG 5056049750560498 GACCCGTTTGGGATGGGAGGTTGCCGCTGGGCTCCTCGCGTTGTGTTTAGGGGAGGAGGA 5056055750560558 CGCAGGGGCCGGGCG

19、CCGCTAGGGGACCCCACCCCCGGGGACAGTCCGGAGCGCTTGGGG 5056061750560618 TCGCCGAGGGGCAGTTCACACTGCGAGTTCAGATTCGGATCGCAGTCCCGATTATCCTCC 5056067750560678 CCTCCAGCCTCTCCCTTTCTCGTTGAAGGGTTAATACAGCGTCCTCTCCCCTCGCCACCC 5056073750560738 GACAGAGGCGCCTACACTGGCGGTAGGTAGCCCCTGGGAGAGGGGGAGTGGGGGGACCCC 5056079750560798 GCC

20、GCTTTCGCCGCTGGGCGACCCAGAGCCCCAGCCTGCCGGAGAGGGCAGCGGCTCGGG 5056085750560858 TTTGACATCCCAGCTGGGTCCCGGGCCGGCTCCCTGAGCCTCCTCCCGGGTTGCTCTCTA 5056091750560918 TCAGGAAAGCAATCGGAAGTCAGGCCGGCTTTTGCTTTTGTTCTGCCAGCTACTCTACGG 5056097750560978 AATCGTAGGTGAAGCCGGGGTGGGCGGATGCCCCGGGAGGGGGCTGTGGCGGGAGTTCCA 50561037

21、50561038 GGTGCGTCCCCGAAATGACCATTGGAGGCGGCGGCTGTTTCCCGCCCCTGGGTGGGGAAT 5056109750561098 GGATTCCGATCGCTAATCGATACCCTGGAGCCAGCAGTGGGTCAGCAGCGTCCCGACAGA 50561157.2. 在Filters的GENE中輸入MAPK4的登錄號，Attributes中選擇輸出六個(gè)物種的旁系同源序列與人類的直系同源序列的蛋白和基因的ID號。將輸出的基因和蛋白ID保存，用于同源序列下載。序列下載時(shí)，先選擇對應(yīng)的Dataset，同源基因Attributes選擇序列（未剪切基因），F(xiàn)ilters的GENE設(shè)為Gene stable ID，同源蛋白下載時(shí)，Attributes選擇序列(peptide)，將Filters的GENE設(shè)為Protein stable ID，將序列導(dǎo)出為fasta格式。（附下載序列）Biomart下載的同源序列登錄號同源序列目標(biāo)基因ID HYPERLINK /homo_sapiens/Gene/Summary?db=core;g=ENSG00000141639 ENSG00000141639同源基因ID同源蛋白ID直系同源序列ENSMPUG00000008813ENSMPUP00000008743ENSF