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人体身高与癌症关联研究的遗传基因知识发现

已有 5920 次阅读 2013-7-26 16:49 |个人分类:知识发现|系统分类:科研笔记| 知识, 遗传基因

terahertz 刘桂锋

许教授,最近对知识发现感兴趣,有时间多指点,谢谢。

刘老师,您好。http://arrowsmith.psych.uic.edu/arrowsmith_uic/index.html 主要用于生物医学领域的知识发现,我不太了解国内外其他学科领域有没有知识发现的系统?我觉得情报界对信息检索与分析已经非常熟悉并重视,但对知识发现不太熟悉和应用。因此我多做些实例介绍,希望科研人员,特别是情报人员能多研究和应用。

人体身高是患癌的风险因素,国际研究文献分析

http://blog.sciencenet.cn/home.php?mod=space&uid=280034&do=blog&quickforward=1&id=711450

 

Start A-Literature C-Literature B-list Filter Literature
A-query: body height
C-query: cancer

The B-list contains title words and phrases (terms) that appeared in both the A and the C literature. 2922 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 # 6307 and can be accessed from the start page after you leave this session. There are 1491 terms on the current B-list (发现413 个遗传基因、蛋白质方面的知识概念,对科研人员也许有所启发和参考价值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.

 

 

 

 

 

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

详细信息  http://arrowsmith.psych.uic.edu/cgi-bin/arrowsmith_uic/view_b_txt.cgi?ID=6307

job id # 6307 started Fri Jul 26 03:39:59 2013
Max_citations: 50000
Stoplist: /var/www/arrowsmith_uic/data/stopwords_pubmed
Ngram_max: 3
A_query_raw: body height Fri Jul 26 03:40:19 2013

A query = body height started Fri Jul 26 03:40:38 2013
C_query_raw: body height Fri Jul 26 03:40:40 2013

C: body height 55383

A query resulted in 50000 titles
A: pubmed_query_A 55383

AC: ( body height ) AND ( body height ) 55383

C_query_raw: cancer Fri Jul 26 03:40:58 2013

C: cancer 2824670

A: pubmed_query_A 55383

AC: ( body height ) AND ( cancer ) 2922

C_query_raw: cancer Fri Jul 26 03:41:01 2013

C: cancer 2824670

A: pubmed_query_A 55383

AC: ( body height ) AND ( cancer ) 2922

C query = cancer started Fri Jul 26 03:41:02 2013
C query resulted in 50000 titles
A AND C query resulted in 2922 titles
32160 B-terms ready on Fri Jul 26 03:43:47 2013

Sem_filter:
Genes & Molecular Sequences, and Gene & Protein Names
1491 B-terms left after filter executed Fri Jul 26 03:44:41 2013

B-list on Fri Jul 26 03:48:56 2013
1 adiponectin
2 fdg
3 pten
4 leptin
5 fat mass
6 promoter polymorphism
7 metabolic syndrome
8 rankl
9 leptin receptor
10 genome wide
11 body mass index
12 hepcidin
13 fmr1
14 microrna
15 jak2
16 polymorphism promoter
17 codon polymorphism
18 polymorphism promoter region
19 ghrelin
20 homeobox
21 single nucleotide polymorphism
22 uncoupling protein
23 bone mineral density
24 sp1
25 promoter polymorphism associated
26 microsatellite
27 ptpn11
28 adiposity
29 calcium sensing receptor
30 aromatase
31 igf i
32 sglt1
33 stat5b
34 ppar gamma
35 hip
36 autophagy
37 gonadotropin releasing hormone
38 igf
39 glut4
40 nod2
41 methylenetetrahydrofolate reductase
42 tandem repeat
43 cftr
44 gstm1
45 igf2
46 cyp2c19
47 igfbp-3
48 methylenetetrahydrofolate reductase gene
49 genome scan
50 fgfr3
51 estrogen receptor
52 nf kappab
53 flt-1
54 cannabinoid receptor
55 melanocortin receptor
56 follistatin
57 cyp2c9
58 ucp2
59 estrogen receptor alpha
60 minisatellite
61 mthfr
62 androgen receptor gene
63 cyp3a
64 mri
65 homeobox gene
66 bdnf
67 lip
68 dax-1
69 cyp19a1
70 contrast enhancement
71 pet
72 body mass
73 hiv
74 socs3
75 nf1
76 androgen receptor
77 exon skipping
78 hrt
79 caspase-9
80 cystatin c
81 diabetes mellitus
82 adrenomedullin
83 timp-1
84 caga
85 leptin gene
86 inflammatory bowel disease
87 receptor gene
88 e polymorphism
89 igfbp-2
90 gdnf
91 gene promoter
92 transcription factor
93 quantitative trait locus
94 sms
95 gli3
96 sox10
97 leptin receptor gene
98 e gene polymorphism
99 hdl
100 caspase-3
101 shc
102 ku
103 ppargamma
104 nsd1
105 myogenin
106 h19
107 myostatin
108 intron
109 genome screen
110 pcr
111 signal regulated kinase
112 glycogen synthase
113 cdk6
114 apolipoprotein e
115 rct
116 yo
117 cyp1a2
118 han
119 osterix
120 runx2
121 ivf
122 pthrp
123 cystatin
124 myostatin gene
125 related gene
126 cytokine
127 hyperparathyroidism
128 eralpha
129 lean body mass
130 exon
131 statin
132 ppar
133 pfos
134 genomic
135 gnas
136 plgf
137 flap
138 hyperinsulinemia
139 q11
140 adiponectin receptor
141 femur
142 mxa
143 snp
144 kruppel factor
145 vitamin d receptor
146 homeodomain protein
147 socs2
148 insulin growth factor
149 collagen induced arthritis
150 lhrh
151 sox10 gene
152 gene family
153 homeobox containing
154 diabetes
155 gene patient
156 growth factor gene
157 gh
158 p53
159 esr2
160 twin
161 q13
162 lh
163 intron polymorphism
164 tnfr2
165 notch1
166 parathyroid hormone
167 collagen gene
168 cyp2b6
169 gnrh
170 mmp-2
171 lmna
172 endothelin
173 node
174 mb
175 pomc
176 promoter
177 anti mullerian hormone
178 lamin
179 estrogen receptor gene
180 g protein
181 intronic
182 fsh
183 promoter haplotype
184 growth hormone receptor
185 tcm
186 functional polymorphism promoter
187 cytokine gene
188 cd34
189 gene cluster
190 ct
191 igfbp-1
192 genome
193 gene col2a1
194 bone morphogenetic protein
195 xa
196 dmh
197 20s
198 cyp17
199 flnb
200 trpv4
201 protein tyrosine phosphatase
202 tgfbeta
203 visfatin
204 g polymorphism
205 candidate gene
206 fasting blood glucose
207 apelin
208 il-6
209 aromatase gene
210 high mobility group
211 transferrin receptor
212 hypercholesterolemia
213 sib
214 cleft lip
215 nph
216 premature ovarian failure
217 egfr
218 cyp1a1
219 precocious
220 celiac disease
221 multiple endocrine neoplasia
222 hmga2
223 immediate early gene
224 rna
225 cag
226 gene encoding
227 dopamine receptor
228 lfa-1
229 race
230 orbit
231 comt
232 apolipoprotein b
233 promoter methylation
234 irs-1
235 ras
236 mc4r
237 tnfalpha
238 promoter region
239 tgf beta
240 meld
241 microsatellite analysis
242 promoter activity
243 apoptosis related gene
244 cd40
245 nail
246 alu
247 ck
248 balloon
249 atrioventricular septal defect
250 polycystic ovary syndrome
251 corticotropin releasing hormone
252 tyrosine phosphatase
253 gerd
254 nijmegen breakage syndrome
255 receptor promoter
256 pparalpha
257 cathepsin k
258 epidermal growth factor
259 obese
260 timp-2
261 copy
262 promoter human
263 rdna
264 fat
265 diabetic nephropathy
266 cytochrome p-450
267 growth hormone
268 laminin
269 adducin
270 tyrosine kinase
271 pth
272 foxc1
273 polymorphism gene
274 lon
275 calpastatin
276 igf-1
277 pdgfra
278 gene environment
279 sirt1
280 seckel syndrome
281 insulin receptor
282 gpcr
283 fasn
284 receptor kinase
285 hsp70
286 dkk1
287 aryl hydrocarbon receptor
288 bmp4
289 bmp-2
290 t4
291 opioid receptor
292 alpha promoter
293 ret
294 gpr30
295 mitochondrial gene
296 glucocorticoid receptor
297 gene expressed
298 p22
299 susceptibility gene
300 signal peptide
301 killer
302 str
303 tgf beta1
304 rev
305 enhancer
306 igfbp-4
307 genomic imprinting
308 apoe
309 gene promoter associated
310 perilipin
311 lean
312 reductase gene
313 fabp2
314 crest
315 long bone
316 igfbp3
317 kinase
318 3d
319 icam-1
320 calpain
321 er alpha
322 codon
323 milk
324 guar
325 factor beta1 gene
326 interleukin
327 cyp11b2
328 sun
329 mmp-9
330 noggin
331 tsh
332 cpap
333 obesity
334 cx43
335 early gene
336 proinsulin
337 klotho
338 chloride channel
339 alpha gene
340 28s
341 e genotype
342 gene chinese
343 sir
344 vldl
345 hyperlipidemia
346 icp
347 alopecia
348 p11
349 factor i
350 col2a1
351 gene familial
352 s100b
353 prolactin
354 copd
355 bph
356 vein
357 sos
358 corn
359 neuropeptide y
360 progesterone receptor
361 carpal tunnel syndrome
362 body weight
363 gene association
364 bak
365 trait
366 ggn
367 hmg coa reductase
368 alfa
369 glucose transporter
370 fibroblast growth factor
371 mscs
372 chi
373 pain
374 connexin
375 tcr
376 domain
377 glutathione s transferase
378 igf1r
379 ghrh
380 lepr
381 hydrocephalus
382 essential tremor
383 opg
384 chd
385 ish
386 polo
387 gen
388 calcitonin receptor
389 klotho gene
390 p21
391 ida
392 decorin
393 cd4
394 tnf alpha
395 ob
396 enpp1
397 ldl
398 human genome
399 apolipoprotein a
400 allele polymorphism
401 esr1
402 ppardelta
403 renal failure
404 ru486
405 whi
406 receptor gene expression
407 breakpoint
408 limb
409 bf
410 titan
411 peroxisome
412 fasting glucose
413 novel gene

 

RANKL与身高研究有3篇文献;与癌症研究有11篇文献。

Start A-Literature C-Literature B-list Filter Literature
AB literature

 

B-term

 

BC literature

 

body height rankl cancer
1: In peripubertal girls, artistic gymnastics improves areal bone mineral density and femoral bone geometry without affecting serum OPG/RANKL levels. 2011
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2: Serum osteoprotegrin (OPG) and receptor activator of nuclear factor kappaB (RANKL) in healthy children and adolescents. 2009
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3: Relationships between osteoprotegerin (OPG), receptor activator of nuclear factor kappaB ligand (RANKL), and growth hormone (GH) secretory status in short children. 2009
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1: Bone metastases in gastric cancer follow a RANKL-independent mechanism. 2013
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2: Targeting RANKL in breast cancer: bone metastasis and beyond. 2013
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3: Progesterone drives mammary secretory differentiation via RankL-mediated induction of Elf5 in luminal progenitor cells. 2013
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4:RANKL Synthesized by Both Stromal Cells and Cancer Cells Plays a Crucial Role in Osteoclastic Bone Resorption Induced by Oral Cancer. 2013
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5: Differential Expression of the RANKL/RANK/OPG System Is Associated with Bone Metastasis in Human Non-Small Cell Lung Cancer. 2013
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6: CCN3 promotes prostate cancer bone metastasis by modulating the tumor-bone microenvironment through RANKL-dependent pathway. 2013
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7: Progesterone/RANKL Is a Major Regulatory Axis in the Human Breast. 2013
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8: A statistical approach for optimization of RANKL overexpression in Escherichia coli: Purification and characterization of the protein. 2013
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9:RANKL Signaling and Osteoclastogenesis Is Negatively Regulated by Cardamonin. 2013
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10:RANKL/RANK/MMP-1 Molecular Triad Contributes to the Metastatic Phenotype of Breast and Prostate Cancer Cells In Vitro. 2013
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11:RANKL promotes the growth of decidual stromal cells in an autocrine manner via CCL2/CCR2 interaction in human early pregnancy. 2013
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RANKL的定义与相关知识和信息如下:

Receptor  Activator for Nuclear Factor-κ B Ligand (核因子κ B受体活化因子配体),又名为TNF-related activation-induced cytokine (TRANCE),TNF相关激活诱导细胞因子;osteoprotegerin ligand (OPGL), 骨保护素配体 osteoclast differentiation factor(ODF ),破骨细胞分化因子。
为避免不同命名在学术上引起不便,美国骨矿研究学会(ASBMR)将其标准化命名为RANKL。
 
Not to be confused with RANK, the osteoclast cell-surface receptor that binds to RANKL.

Receptor activator of nuclear factor kappa-B ligand (RANKL), also known as tumor necrosis factor ligand superfamily member 11 (TNFSF11), TNF-related activation-induced cytokine (TRANCE), osteoprotegerin ligand (OPGL), and osteoclast differentiation factor (ODF), is a protein that in humans is encoded by the TNFSF11gene.[1][2]

Critical for adequate bone metabolism, this surface-bound molecule (also known as CD254) found on osteoblasts serves to activate osteoclasts, which are the cells involved in bone resorption. Osteoclastic activity is triggered via the osteoblasts' surface-bound RANKL activating the osteoclasts' surface-bound receptor activator of nuclear factor kappa-B (RANK).

Function[edit]

RANKL is a member of the tumor necrosis factor (TNF) cytokine family which is a ligand for osteoprotegerin and functions as a key factor for osteoclast differentiation and activation. RANKL also has a function in the immune system, where it is expressed by T helper cells and is thought to be involved in dendritic cell maturation. This protein was shown to be a dendritic cell survival factor and is involved in the regulation of T cell-dependent immune response. T cell activation was reported to induce expression of this gene and lead to an increase of osteoclastogenesis and bone loss. This protein was shown to activate antiapoptotic kinase AKT/PKB through a signaling complex involving SRC kinase and tumor necrosis factor receptor-associated factor 6 (TRAF6), which indicated this protein may have a role in the regulation of cell apoptosis.[3]

Animal models[edit]

Targeted disruption of the related gene in mice led to severe osteopetrosis and a lack of osteoclasts. The deficient mice exhibited defects in early differentiation of T and B lymphocytes, and failed to form lobulo-alveolar mammary structures during pregnancy.[3]

Clinical significance[edit]Bone[edit]

Overproduction of RANKL is implicated in a variety of degenerative bone diseases, such as rheumatoid arthritis and psoriatic arthritis. The first FDA-approved RANKL inhibitor was denosumab (to treat osteoporosis in post menopausal women).

Breast cancer[edit]

Treatment with medroxyprogesterone acetate (MPA), a synthetic progestin that is used in birth control pills and hormone replacement therapy, is associated with an increased risk of developing breast cancer. MPA causes a substantial induction of RANKL in mammary-gland epithelial cells while deletion of RANKL decreases the incidence MPA-induced breast cancer. Hence inhibition of RANKL has potential for the prevention and treatment of breast cancer.[4][5]

See also[edit] References[edit]
  1. ^Wong BR, Rho J, Arron J, Robinson E, Orlinick J, Chao M, Kalachikov S, Cayani E, Bartlett FS, Frankel WN, Lee SY, Choi Y (October 1997). "TRANCE is a novel ligand of the tumor necrosis factor receptor family that activates c-Jun N-terminal kinase in T cells". J. Biol. Chem.272 (40): 25190–4. doi:10.1074/jbc.272.40.25190. PMID 9312132. 

  2. ^Anderson DM, Maraskovsky E, Billingsley WL, Dougall WC, Tometsko ME, Roux ER, Teepe MC, DuBose RF, Cosman D, Galibert L (November 1997). "A homologue of the TNF receptor and its ligand enhance T-cell growth and dendritic-cell function". Nature390 (6656): 175–9. doi:10.1038/36593. PMID 9367155. 

  3. ^ ab"Entrez Gene: TNFSF11 tumor necrosis factor (ligand) superfamily, member 11". 

  4. ^Schramek D, Leibbrandt A, Sigl V, Kenner L, Pospisilik JA, Lee HJ, Hanada R, Joshi PA, Aliprantis A, Glimcher L, Pasparakis M, Khokha R, Ormandy CJ, Widschwendter M, Schett G, Penninger JM (November 2010). "Osteoclast differentiation factor RANKL controls development of progestin-driven mammary cancer". Nature468 (7320): 98–102. doi:10.1038/nature09387. PMID 20881962. 

  5. ^Gonzalez-Suarez E, Jacob AP, Jones J, Miller R, Roudier-Meyer MP, Erwert R, Pinkas J, Branstetter D, Dougall WC (November 2010). "RANK ligand mediates progestin-induced mammary epithelial proliferation and carcinogenesis". Nature468 (7320): 103–7. doi:10.1038/nature09495. PMID 20881963. 

Further reading[edit]
External links[edit]

This article incorporates text from the United States National Library of Medicine, which is in the public domain.

 



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