Sample output 1

The table below represents a ranked list of terms extracted automatically from a corpus of PubMed abstracts in molecular biology. Term variants grouped together in the second column represent lowercased versions of all surface forms found in the corpus. For each term, the variants are ordered by their frequency of occurrence in the corpus. The score in the rightmost column is called termhood and is calculated as a function of frequency and length (in tokens minus stopwords). Alternatively, you may view the results as a dendrogram produced by the clustering algorithm described in this paper.

Rank Term variants Score
1 tnf-alpha
tnf
tumor necrosis factor alpha
tnf alpha
 84.9717
2 tumor necrosis factor
 74.6058
3 nf-kappa b
nf-kappab
nf kappa b
nuclear factor-kappa b
nuclear factor kappa b
nuclear factor kappab
nuclear factor-kappab
 52.8846
4 transcription factor
transcription factors
transcriptional factors
 48.3744
5 gene expression
expression of genes
 27.6150
6 activation of nf-kappa b
nf-kappa b activation
nf-kappa b activity
nf-kappab activation
nf-kappab activity
 27.0991
7 glucocorticoid receptors
gr
glucocorticoid receptor
gcr
 23.5237
8 human t cells
human cells
 23.5208
9 protein kinase
 23.3360
10 cbf
core binding factor
 22.7962
11 transcriptional activity
activator of transcription
transcriptional activation
activating transcription
activators of transcription
transcription activation
transcriptional activator
 22.1807
12 gm-csf
granulocyte-macrophage colony-stimulating factor
 20.8736
13 electrophoretic mobility shift assays
emsa
electrophoretic mobility shift assay
emsas
 20.7944
14 ra
retinoic acid
 20.2746
15 cell lines
cell line
 19.4081
16 human monocytes
 19.1528
17 hiv
human immunodeficiency virus
 17.0895
18 binding factors
 16.9388
19 pma
phorbol myristate acetate
 15.3806
19 pkc
protein kinase c
 15.3806
19 ptk
protein tyrosine kinase
protein tyrosine kinases
 15.3806
20 peripheral blood
 15.3648
21 tyrosine kinase
 13.4297
22 means of electrophoretic shift assay
 12.8171
23 b cells
 12.4766
23 monocytic cells
 12.4766
24 tyrosine phosphorylation
 12.3506
25 activator protein
activator protein-1
ap
 12.3167
26 icam-1
intercellular adhesion molecule-1
 11.9278
27 cell activation
activation of t cells
 11.7340
28 rar
retinoic acid receptor
 11.4256
29 signal transducer
signal transducers
signal transduction
 11.0904
30 er
estrogen receptor
estrogen receptors
 10.9517
31 nuclear factor
 10.8593
32 cbf alpha
 10.8131
33 erythroid cells
 10.2239
34 pbl
peripheral blood lymphocytes
 9.8875
35 tnf-alpha release in human monocytes
 9.7296
36 ar
androgen receptors
 9.7041
36 gene transcription
transcription of genes
 9.7041
37 tnf-alpha release
 9.6566
38 binding site
binding sites
 9.5060
39 rxr
retinoid x receptor
 9.4481
40 dna binding activity
dna-binding activity
 9.0109
41 human t lymphocytes
 8.9532
42 tnf alpha mrna
tnf mrna
 8.8519
43 pbmo
peripheral blood monocytes
 8.7889
44 jurkat cells
jurkat t cells
 8.3178
45 cell cycle
 8.1791
46 tf
tissue factor
 8.0207
47 endothelial cells
 7.4860
47 ifn-gamma
interferon gamma
 7.4860
48 kappa b
 7.2285
49 lps-induced nf-kappab activation
 6.9315
49 nuclear extracts
 6.9315
49 mdhm
mycoplasma fermentans-derived high-molecular-weight material
 6.9315
50 activation of protein kinases
 6.8663
51 b lymphocytes
 6.8325
51 regulatory elements
regulatory element
 6.8325
52 ebv
epstein-barr virus
 6.7928
53 ckii
casein kinase ii
 6.5917
53 erk
extracellular signal-regulated kinase
 6.5917
54 retinoic acid receptor alpha
rar alpha
 6.2383
54 binding activity
 6.2383
54 t-cell activation
 6.2383
54 response element
 6.2383
55 transcriptional regulation
transcriptional regulator
 6.1393
56 ctl
cytotoxic t-lymphocyte
 6.0650
57 myristate acetate
 5.8918
58 protein tyrosine kinase activity
protein tyrosine kinase activation
 5.5452
58 cbf beta
 5.5452
58 icer
inducible camp early repressor
 5.5452
58 nrds
neonatal respiratory distress syndrome
 5.5452
59 all-trans retinoic acid
atra
 5.4931
59 activation of transcription factors
 5.4931
59 nuclear nf-kappa b
 5.4931
59 nf-kappa b protein
 5.4931
59 cd28re
cd28 response element
 5.4931
60 cell surface
surface of intact t cells
 4.8520
60 il-2 production
 4.8520
60 t-cell lines
t-cell line
 4.8520
61 cat
chloramphenicol acetyl-transferase
 4.7134
61 lytic cycle
 4.7134
62 promoter activity
 4.5748
63 kappa b enhancer
kappa b enhancers
 4.3944
63 b transcription factors
 4.3944
63 monocytic thp-1 cells
 4.3944
63 cepsilon germline transcripts
 4.3944
63 erythroid-specific gene expression
expression of erythroid-specific genes
 4.3944
63 ihes
idiopathic hypereosinophilic syndrome
 4.3944
64 activation of genes
gene activity
 4.1589
64 tcf-1 alpha binding site
 4.1589
64 differentiated cells
cell differentiation
differentiation of t cells
 4.1589
64 cell responses
cells in response
 4.1589
64 coproporphyrinogen oxidase
cpo
 4.1589
64 lps-induced nf-kappab dna
 4.1589
64 transcription factor nf-kappab
transcription factor nuclear factor-kappa b
transcription factor nuclear factor-kappab
 4.1589
64 family proteins
ets protein family
family of proteins
 4.1589
64 globin promoter
globin promoters
 4.1589
64 hiv type
human immunodeficiency virus type
 4.1589
64 il-2 receptor
il-2r
 4.1589
65 tnf-alpha production
 4.0236
66 epithelial cells
 3.9856
66 inhibitor protein
inhibitory protein
 3.9856
67 gene in t cells
genes in t cells
genes of t cells
 3.9278
68 tnf mrna accumulation
 3.5835
69 lps-induced activity
 3.4657
69 cell adhesion
 3.4657
69 il-1 beta
 3.4657
69 cell functions
functions of cells
 3.4657
69 murine t cells
 3.4657
69 cell receptor
 3.4657
69 thp-1 cells
 3.4657
69 u937 cells
 3.4657
69 cytokine genes
 3.4657
69 pge2
prostaglandin e2
 3.4657
69 p elements
p element
 3.4657
69 p-like elements
 3.4657
69 embryonic-fetal liver
fl
 3.4657
69 induction of expression
 3.4657
69 surface expression
 3.4657
69 gene induction
 3.4657
69 il-2 promoter
 3.4657
69 immune system
 3.4657
69 nuclear proteins
 3.4657
69 nuclear translocation
 3.4657
69 stat proteins
 3.4657
70 il-1beta promoter activity
 3.2958
70 acute promyelocytic leukemia
apl
 3.2958
70 tcr alpha enhancer
 3.2958
70 kappa b-like site
 3.2958
70 bronchial epithelial cells
 3.2958
70 erythroid cell survival
 3.2958
70 human monocytic cells
 3.2958
70 polymerase chain reaction
pcr
 3.2958
70 tf gene
 3.2958
70 tf site
 3.2958
70 ifn-gamma production
production of ifn-gamma
 3.2958
70 gamma response region
grr
 3.2958
70 syk tyrosine kinase
tyrosine kinase syk
 3.2958
70 serine phosphorylation of stat3
 3.2958
71 transient expression
 3.2924
72 il-9 gene
 3.2347
72 hiv-1 replication
 3.2347
73 cbf alpha subunit
 3.2189
74 tcf-1 alpha
 3.0036
74 blood cells
 3.0036
75 enhanced activity
enhancer activity
 2.7726
75 activation in t lymphocytes
activity of lymphocytes
lymphocyte activation
 2.7726
75 alpha b
 2.7726
75 binding proteins
 2.7726
75 human peripheral blood monocytes
 2.7726
75 monocytic thp-1 cell line
 2.7726
75 myeloid cells
 2.7726
75 nonerythroid cells
 2.7726
75 cell types
cell type
 2.7726
75 nuclear compartment
nuclear compartments
 2.7726
75 nuclear complex
nuclear complexes
 2.7726
75 pdtc
pyrrolidine dtc
 2.7726
75 phorbol ester
 2.7726
75 expression of il-2
il-2 expression
 2.7726
75 family members
 2.7726
75 plc gamma
 2.7726
75 human leukemias
 2.7726
75 immune response
immune responses
 2.7726
75 oxldl
oxidized ldl
 2.7726
75 neutrophil maturation
 2.7726
75 rel proteins
 2.7726
76 cat reporter
 2.7465
77 reporter gene
 2.5415
78 50-kda nf-kappa b
 2.1972
78 activation of human t cells
activities on human t cells
 2.1972
78 androgen receptor gene
 2.1972
78 expression of cd40 antigen
 2.1972
78 ap-1 transcription factor
transcriptional factors ap-1
 2.1972
78 patients with hepatitis b
 2.1972
78 beta interferon promoter
 2.1972
78 dna binding motif
 2.1972
78 dna binding specificities
 2.1972
78 fetal blood cells
 2.1972
78 cord blood lymphocytes
 2.1972
78 phospholipase c gamma
 2.1972
78 erythroid cell development
 2.1972
78 human mononuclear cells
 2.1972
78 kappa light chain
 2.1972
78 lytic cycle genes
 2.1972
78 nf-kappab dna
 2.1972
78 regulation of gene expression
 2.1972
78 hematopoietic growth factor
hgf
 2.1972
78 nf-kappab inhibitors
 2.1972
78 fish
fluorescence in situ hybridization
 2.1972
78 gr in lymphocytes
 2.1972
78 normal human monocytes
 2.1972
78 rna polymerase ii
 2.1972
78 protein kinase inhibition
 2.1972
79 94-kd stat5a
 2.0794
79 amino acids
 2.0794
79 activation of ap-1
 2.0794
79 activity of dna
 2.0794
79 ltr activation
 2.0794
79 activation of nf-at
nf-at activation
 2.0794
79 stat3 activation
 2.0794
79 monocyte adhesion
 2.0794
79 receptor alpha chain
receptor alpha-chain
 2.0794
79 cd40 antigen
 2.0794
79 induction of apoptosis
 2.0794
79 monocyte apoptosis
 2.0794
79 nf-kappa b1
 2.0794
79 c-fos expression
 2.0794
79 caccc-binding proteins
 2.0794
79 cell cultures
 2.0794
79 normal cells
normal t cell
 2.0794
79 primary cells
 2.0794
79 tolerant cells
 2.0794
79 transcription in t cells
 2.0794
79 cellular proliferation
 2.0794
79 il-4ralpha chain
 2.0794
79 clonal eosinophilia
 2.0794
79 cytokine production
production of cytokines
 2.0794
79 histone deacetylase
 2.0794
79 dose-dependent manner
 2.0794
79 se
staphylococcal enterotoxin
 2.0794
79 environmental estrogens
 2.0794
79 globin gene
 2.0794
79 immediate-early genes
 2.0794
79 il-4 promoter
 2.0794
79 il-4 receptor
il-4r
 2.0794
79 inflammatory response
inflammatory responses
 2.0794
79 physical linkage
 2.0794
79 lps response
lps responsiveness
 2.0794
79 lps stimulation
 2.0794
79 site-directed mutagenesis
 2.0794
79 viral production
 2.0794
79 sodium salicylate
 2.0794
79 transient transfection
 2.0794
80 cell development
 1.7329
80 zinc fingers
 1.7329
80 il-13 gene
 1.7329
80 situ hybridization
 1.7329
80 sm protein
 1.7329
81 icam-1 kappa b
 1.6094
82 1,25-dihydroxyvitamin d3
24,25-dihydroxyvitamin d3
 1.3863
82 agonist activity
 1.3863
82 alpha activity
 1.3863
82 hydrolytic activity
 1.3863
82 potent activator
 1.3863
82 bind with higher affinity
binding affinity
 1.3863
82 aldosterone receptors
 1.3863
82 pebp2 alpha
 1.3863
82 humara analysis
 1.3863
82 anti-cd3 stimulation
 1.3863
82 ap-1 site
 1.3863
82 supershift assay
 1.3863
82 beas-2b cells
 1.3863
82 dendritic cell
 1.3863
82 hela cells
 1.3863
82 hl60 cells
 1.3863
82 k562 cells
 1.3863
82 mo7e cells
 1.3863
82 naive th cells
 1.3863
82 cell population
cell populations
 1.3863
82 cell proliferation
 1.3863
82 unprimed cells
 1.3863
82 complex in response
 1.3863
82 cox-2 expression
 1.3863
82 erythroid differentiation
 1.3863
82 dna sequences
 1.3863
82 dna binding subunit
dna-binding subunit
 1.3863
82 inducible expression
 1.3863
82 rantes expression
 1.3863
82 expression of certain transcription
expression of transcription
 1.3863
82 il-4 gene
il-4 genes
 1.3863
82 saa gene
 1.3863
82 tyrosine kinase inhibitors genistein
 1.3863
82 hiv-1 ltr
 1.3863
82 p50 homodimer
p50 homodimers
 1.3863
82 steroid hormone
 1.3863
82 human interleukin
 1.3863
82 human thymocytes
 1.3863
82 hypertensive patients
patients with hypertension
 1.3863
82 induction of vcam-1
 1.3863
82 janus kinase
 1.3863
82 lai ltr
 1.3863
82 mononuclear leukocytes
 1.3863
82 microbial lipoproteins
 1.3863
82 lps tolerance
 1.3863
82 ltr sequence
 1.3863
82 plasma membrane
 1.3863
82 molecular weight
 1.3863
82 x-inactivation patterns
 1.3863
82 tax protein
 1.3863
82 transient pseudohypoaldosteronism
 1.3863
82 tlrs
toll-like receptors
 1.3863
82 superoxide release
 1.3863
82 steroid treatments
 1.3863
83 human endothelial cells
 1.0986
83 heterodimer complex formation
 1.0986
83 respiratory distress syndrome
 1.0986
84 natl. acad
 0.6931
84 cd3 ligation
 0.6931
84 cell survival
 0.6931
84 cytokine profiles
 0.6931
84 hypereosinophilic syndrome
 0.6931
84 il-1beta promoter
 0.6931