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青光眼基因的知识发现

已有 2183 次阅读 2014-6-16 10:16 |个人分类:知识发现|系统分类:科研笔记



科研思路来自科研实践、来自文献信息、来自同行交流。

      科研思路和科研选题也可以来自知识发现,在我的博客“知识发现栏目”http://blog.sciencenet.cn/home.php?mod=space&uid=280034&do=blog&classid=115378&view=me&from=space有大量的科学研究知识发现的实例和分析,知识发现只提供非相关文献中的隐含知识概念,对于扩大科研人员的研究思路、进行科研选题很有意义,这些知识点可能对科研工作有所启发,获得新的科研视角和思路,但还需要科研人员进行科学验证。

知识发现与科学发现  http://blog.sciencenet.cn/blog-280034-713521.html

      这里可以看到自1986年以来,国外情报专家的很多知识发现,被科研人员得到了证实。但我国的科研人员对知识发现的方法和应用不太熟悉,还没有很好地利用这种知识挖掘和信息分析的好方法。

最新研究进展

千年基因携手中山大学眼科中心通过高质量的外显子组测序及数据挖掘,揭示了青光眼致病相关的基因,相关成果发表于眼科研究领域的著名杂志IOVS。

千年基因对本研究中257个青光眼患者提供了高质量的外显子组测序,其中包括36个青少年开角型青光眼(JOAG)、89个原发性开角型青光眼(POAG)及132个原发性闭角型青光眼(PACG)。通过对测序数据的变异分析,在20个患者中检测到39个变异位点,分别来自MYOC、WDR36、OPTN及OPA1四个基因。经Sanger测序验证得知其中36个变异是正确的,阳性验证率高达92%。通过致病性分析发现,19个变异信息是与青光眼致病相关的,其中5个是已报道过的,14个是新发现的变异。

知识发现平台 http://arrowsmith.psych.uic.edu/cgi-bin/arrowsmith_uic/edit_b.cgi

 

A-query: glaucoma
C-query: MYOC OR WDR36 OR OPTN OR OPA1

The B-list contains title words and phrases (terms) that appeared in both the A and the C literature. 414 articles appeared in both literatures and were not included in the process of computing the B-list but can be viewed here. The results of this search are saved under id # 7288 and can be accessed from the start page after you leave this session. There are 265 terms on the current B-list (45 are predicted to be relevant), which is shown ranked according to predicted relevance. The list can be further trimmed down using the filters listed in the left margin.

To assess whether there appears to be a biologically significant relationship between the AB and BC literatures for specific B-terms, please select one or more B-terms and then click the button to view the corresponding AB and BC literatures. Use Ctrl to select multiple B-terms.

job id # 7288 started Sun Jun 15 21:01:15 2014
Max_citations: 50000
Stoplist: /var/www/arrowsmith_uic/data/stopwords_pubmed
Ngram_max: 3
A_query_raw: glaucomaSun Jun 15 21:01:22 2014

A query = glaucoma started Sun Jun 15 21:01:22 2014
A query resulted in 50000 titles
C_query_raw: glaucoma Sun Jun 15 21:01:27 2014

C: glaucoma 53686

A: pubmed_query_A 53686

AC: ( glaucoma ) AND ( glaucoma ) 53686

C_query_raw: MYOC OR WDR36 OR OPTN OR OPA1 Sun Jun 15 21:02:15 2014

C: MYOC OR WDR36 OR OPTN OR OPA1 1325

A: pubmed_query_A 53686

AC: ( glaucoma ) AND ( MYOC OR WDR36 OR OPTN OR OPA1 ) 414

C_query_raw: MYOC OR WDR36 OR OPTN OR OPA1 Sun Jun 15 21:02:18 2014

C: MYOC OR WDR36 OR OPTN OR OPA1 1325

A: pubmed_query_A 53686

AC: ( glaucoma ) AND ( MYOC OR WDR36 OR OPTN OR OPA1 ) 414

C query = MYOC OR WDR36 OR OPTN OR OPA1 started Sun Jun 15 21:02:18 2014
C query resulted in 1325 titles
A AND C query resulted in 414 titles
2809 B-terms ready on Sun Jun 15 21:09:51 2014

Sem_filter:
Genes & Molecular Sequences, and Gene & Protein Names
265 B-terms left after filter executed Sun Jun 15 21:12:55 2014

B-list on Sun Jun 15 21:17:28 2014
1 myocilin
2 optineurin
3 tigr
4 myopia
5 caspase
6 genome wide
7 akt
8 promoter polymorphism
9 lumican
10 optic atrophy
11 cdna
12 tigr gene
13 hla
14 pax6
15 rapd
16 cdna a
17 exon
18 single nucleotide polymorphism
19 mtor
20 gene chinese
21 drp1
22 nf kappab
23 diabetes mellitus
24 olfactomedin
25 candidate gene
26 gene encoding
27 wfs1 gene
28 wfs1
29 transcription factor
30 bax
31 diabetes
32 alzheimer disease
33 glucocorticoid receptor
34 progressive external ophthalmoplegia
35 cdk5
36 cytokine
37 sod1
38 leptin
39 codon
40 race
41 genome
42 bak
43 gene patient
44 autophagy
45 domain

http://arrowsmith.psych.uic.edu/cgi-bin/arrowsmith_uic/view_b_txt.cgi?ID=7288

 

StartA-LiteratureC-LiteratureB-listFilterLiterature
AB literature


B-term


BC literature


glaucomatigrMYOC OR WDR36 OR OPTN OR ...
1: Focus on Molecules: Myocilin/TIGR. 2005
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2: Only neutral polymorphisms found in the TIGR/myocilin gene of 45 Polish patients with primary open-angle glaucoma. 2004
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3: [Study of TIGR gene in patients with primary open angle glaucoma] 2004
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4:TIGR is upregulated in the chronic glial scar in response to central nervous system injury and inhibits neurite outgrowth. 2003
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5: [Study on the gene mutation of TIGR in primary open angle glaucoma, their relatives and normal controls in Chongqing] 2003
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6: A multidomain TIGR/olfactomedin protein family with conserved structural similarity in the N-terminal region and conserved motifs in the C-terminal region. 2002
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7: [Study on single nucleotide polymorphism of TIGR gene in primary open-angle glaucoma patients] 2002
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8: Reduced TIGR/myocilin protein in the monkey ciliary muscle after topical prostaglandin F(2alpha) treatment. 2001
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9: Expression of myocilin/TIGR in normal and glaucomatous primate optic nerves. 2001
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10: Novel TIGR sequence alteration Val53Ala. 2000
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11: Truncations in the TIGR gene in individuals with and without primary open-angle glaucoma. 2000
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12: [The attempt to identify mutations in TIGR gene in Polish patients with primary open angle glaucoma] 2000
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13: [To screen, clone and sequence TIGR gene mutation in Chinese patients with primary open- angle glaucoma] 2000
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14: Detection of a new TIGR gene mutation in a Japanese family with primary open angle glaucoma. 1999
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15: Immunofluorescence method for quantifying the trabecular meshwork glucocorticoid response (TIGR) protein in trabecular meshwork and Schlemm's canal cells. 1999
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16: Juvenile open angle glaucoma: fine mapping of the TIGR gene to 1q24.3-q25.2 and mutation analysis. 1998
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17: Gene structure and properties of TIGR, an olfactomedin-related glycoprotein cloned from glucocorticoid-induced trabecular meshwork cells. 1998
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18: Novel mutations in the TIGR gene in early and late onset open angle glaucoma. 1998
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19: Characterization of the murine TIGR/myocilin gene. 1998
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20: Homozygotes carrying an autosomal dominant TIGR mutation do not manifest glaucoma. 1998
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21: Prevalence of mutations in TIGR/Myocilin in patients with adult and juvenile primary open-angle glaucoma. 1998
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22: The TIGR gene, pathogenic mechanisms, and other recent advances in glaucoma genetics. 1998
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23: Cloning and characterization of subtracted cDNAs from a human ciliary body library encoding TIGR, a protein involved in juvenile open angle glaucoma with homology to myosin and olfactomedin. 1997
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24: Recurrent mutations in a single exon encoding the evolutionarily conserved olfactomedin-homology domain of TIGR in familial open-angle glaucoma. 1997
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25: Mutations in the TIGR gene in familial primary open-angle glaucoma in Japan. 1997
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26: Identification of a new 'TIGR' mutation in a family with juvenile-onset primary open angle glaucoma. 1997
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27:TIGR gene in primary open-angle glaucoma and steroid-induced glaucoma. 1997
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1: Effects of elevated intraocular pressure on outflow facility and TIGR/MYOC expression in perfused human anterior segments. 2002
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2: Changes in mRNA levels of the Myoc/Tigr gene in the rat eye after experimental elevation of intraocular pressure or optic nerve transection. 2001
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3: Recombinant TIGR/MYOC increases outflow resistance in the human anterior segment. 2000
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