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PHOX2B (paired-like homeobox 2b)

Written2013-04Tiziana Bachetti, Isabella Ceccherini
UOC Medical Genetics, G Gaslini Institute, 16147 Genova, Italy

(Note : for Links provided by Atlas : click)


Other aliasNBLST2
LocusID (NCBI) 8929
Atlas_Id 126
Location 4p13  [Link to chromosome band 4p13]
Location_base_pair Starts at and ends at bp from pter
Local_order APBB2 - UCHL1 - LIMCH1 - PHOX2B - TMEM33 - DCAF4L1 - ATP1B1P1 - SLC30A9.
  Cytogenetic location of PHOX2B on chromosome 4.
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)


Note Genomic: NCBI Reference Sequence: NG_008243.1.
  PHOX2B gene structure: untranslated regions (orange boxes), introns (black lines) and coding regions (blue boxes) are shown.
Description The PHOX2B gene is 4888bp long; the coding region (CDS) is 945bp and is composed of 3 exons: exon 1 (241bp), exon 2 (188bp), exon 3 (516bp).
Other features: 5'UTR: 361bp; 3'UTR: 1725bp.
Transcription mRNA: NCBI Reference Sequence NM_003924.3. The PHOX2B mRNA is 3218bp long; no alternative splice site is known.
Pseudogene No pseudogene is reported.


Note NCBI Reference Sequence: NP_003915.2.
  Representation of the PHOX2B protein. The three exons (blue) are shown, with the number of aminoacids (aa) they code for, in addition to the homeodomain (red) and the polyalanine stretches (yellow). In the upper part of the figure, the first and last aminoacid positions for each of these crucial regions is indicated.
Description PHOX2B protein is 314 aminoacids long. A homeodomain region spanning exons 1 and 2 (from residue 99 to residue 148) is responsible for the binding of this transcription factor to target DNA elements. In exon 3 there are two sequences characterized by stretches of 9 and 20 alanine residues, encoded by GC(N) triplets. Their functional role is still unknown.
Expression PHOX2B is expressed during neural development in central autonomic circuits and peripheral neural crest derivatives, and particularly in the retrotrapezoid nucleus, noradrenergic centres and hindbrain (Pattyn et al., 1997; Dubreuil et al., 2002; Stornetta et al., 2006; Kang et al., 2007).
PHOX2B expression is transcriptionally regulated by the PHOX2B protein itself, through its direct binding to four promoter elements which give rise to a positive autoregulatory loop (Cargnin et al., 2005). In addition, PHOX2B expression is known to be regulated at specific sympathetic and enteric nervous system developmental stages by E2a and Hand2 (Hashimoto et al., 2011). Finally, SOX10 (Nagashimada et al., 2012), as well as PHOX2A and HASH1 (reviewed by Brunet and Pattyn, 2002) have shown a degree of cross-regulation with respect to PHOX2B. Hoxb1 and Hoxb2 have also shown to form a trimer with Pbx1 and Meis 1 to regulate PHOX2B transcription (Samad et al., 2004).
Localisation PHOX2B is localized within the nuclear compartment.
Function PHOX2B is a transcription factor essential for the development of autonomic neural crest derivatives (Pattyn et al., 1999). It controls the development of motoneurons (Pattyn et al., 2000) and drives a somatic-to-visceral switch in cranial sensory pathways (D'Autréaux et al., 2011).
PHOX2B regulates the transcriptional expression of several genes: TH (Lo et al., 1999), DBH (Adachi et al., 2000), PHOX2A (Flora et al., 2011), PHOX2B itself (Cargnin et al., 2005), RET (Bachetti et al., 2005a), TLX-2 (Borghini et al., 2006), ALK (Bachetti et al., 2010), SOX10 (Nagashimada et al., 2012), Hand1 (Vincentz et al., 2012), SCG2 (Wen et al., 2007), MSX1 (Revet et al., 2008).
CREB-binding protein (CREBBP/CBP) interacts with PHOX2B and serves as its coactivator to mediate synergistic trans-activation (Wu et al., 2009). Using a yeast two-hybrid screening, TRIM11 was isolated as an additional PHOX2B interacting protein (Hong et al., 2008).
Homology The amino acid sequence of the human PHOX2B is 100% identical to those of the chimpanzee, rat and mouse, suggesting that the function of PHOX2B is highly conserved in Mammals.


Note There is a clear correlation between types of PHOX2B mutations and clinical manifestations. Indeed, while the vast majority of PHOX2B mutations identified in isolated Congenital Central Hypoventilation Syndrome (CCHS) are PARMs (Polyalanine repeats mutation), those present in HSCR-NB (Hirschsprung's disease-neuroblastoma) associated CCHS are non-PARMs (NPARM), namely either missense mutations or nucleotide deletions/insertions causing frameshifts of the open reading frame. Moreover, inherited and de novo missense and frameshift mutations in exons 2 and 3 of the PHOX2B gene have been detected in both sporadic (NB) and syndromic (NB+CCHS) cases (Weese-Mayer et al., 2010; Bachetti et al., 2005b), thus suggesting that PHOX2B may play a role in isolated NB pathogenesis.
  Fig.4: Localization of mutations within the PHOX2B gene. In the figure some PARMS (yellow) and NPARMS (black) PHOX2B mutations are shown (see also Weese-Mayer et al., 2010).
Table 1: NPARMS and PARMS mutations of PHOX2B in human disease. Table 1 reports PHOX2B mutations detected so far, with detailed description of the nucleotide and aminoacid changes. Associated phenotypes are also annotated. Legend: NB neuroblastoma, TSNS tumor sympathetic nervous system, CCHS congenital central hypoventilation syndrome, LO-CHS late onset central hypoventialtion syndrome, NF1 neurofibromatosis type 1, (?) undetermined associations.
Germinal Germline PHOX2B mutations are responsible for Congenital Central Hypoventilation Syndrome (CCHS). The vast majority of mutations is represented by in frame triplet duplications of a sequence stretch coding for 20 Alanine residues in exon 3, also known as polyalanine (polyAla) expansions or PARM (Polyalanine repeats mutation). The duplication length is variable, starting from 12 bp up to 39 bp, thus leading from +4 Ala up to +13 Ala expansions (Amiel et al., 2003; Sasaki et al., 2003; Weese-Mayer et al., 2003; Matera et al., 2004; Trochet et al., 2008a).
Ninety percent of constitutive (germinal) mutations detected in CCHS patients are represented by polyAla expansions. Among these, 75% have arisen de novo while 25% is inherited from one parent (Bachetti et al., 2011; Meguro et al., 2012).
In addition, germline PHOX2B missense, frameshift, nonsense non polyAla mutations (NPARMs) have been detected in a small fraction of mainly syndromic patients characterized by CCHS+other neurocristophaties such as neuroblastoma (NB) and/or Hirschsprung's disease (HSCR) (Trochet et al., 2005; Matera et al., 2004). A few specific missense PHOX2B mutations have been detected in isolated NB and/or HSCR, as reported in Table 1.
In frame deletions within the polyAla stretch have been identified in healthy subjects, but also in association with schizophenia (Toyota et al., 2004).
Somatic No CCHS patient has ever been proven to be a somatic mosaic for PHOX2B mutation; however, somatic and therefore germline mosaicism has been demonstrated in a proportion of CCHS parents (Parodi et al., 2008; Bachetti et al., 2011; Bachetti et al., 2013).
Somatic PHOX2B mutations have been identified in NB cell lines and NB tumor samples as reported in the Table 1.

Implicated in

Entity PARMs (from +4 to +13 polyAla expansions)
Note A correlation between the length of the expanded tract and the severity of the CCHS phenotype has already been reported (Matera et al., 2004; Weese-Mayer et al., 2010). Additional dysfunction of the autonomous nervous system, such as HSCR, NB, ocular defects, cardiac rythm alterations, etc., may be found in association with the especially largest polyAla expansions (Weese-Mayer et al., 2010).
Disease Congenital Central Hypovention Syndrome (CCHS).
Prognosis Congenital central hypoventilation syndrome (CCHS) is characterized by alveolar hypoventilation and autonomic dysregulation. It is a life-long, still untreatable disease.
Oncogenesis Among PARMs, only subjects with the 20/29 and 20/33 genotypes have been identified to have tumors of neural crest origin (ganglioneuromas and ganglioneuroblastomas). No children with genotypes 20/24 to 20/28 have been identified with tumors of neural crest origin (Weese-Mayer et al., 2010).
Entity NPARMS: non polyAla repeat mutations, either germline or somatic (i.e. missense, nonsense, indels and loss of the stop codon mutations)
Note These mutations, listed in Table 1, include missense, nonsense, loss of stop codon and small indels mutations.
Disease Neuroblastoma and/or Hirschsprung's disease (either sporadic or in association with CCHS).
Entity Neuroblastoma
Note In neuroblastoma cell lines and tumor samples, PHOX2B expression has turned out to be much higher than in normal tissues (Longo et al., 2008). Moreover, LOH in about 10% of the tumors and rare aberrant CpG dinucleotide methylation of 500bp of PHOX2B promoter region have been reported as NB associated molecular event (De Pontual et al., 2007).


Note A 5-Mb deletion at chromosome 4p12-p13 that included the PHOX2B gene was found in a 16-month-old girl with developmental delay, severe hypotonia, facial dysmorphism, and short-segment Hirschsprung disease thus suggesting that PHOX2B haploinsufficiency may predispose to colonic aganglionosis (Benailly et al,. 2003).
Interestingly, other cytogenetic interstitial deletions, spanning from 0.29 to 2.6 Mb across the PHOX2B locus, have been detected in patients affected with atypical disorders, apparently sharing a loss of function/haploinsufficiency pathogenic mechanism, namely apparent-life threatening event including, Hirschsprung disease, transient neonatal hypoventilation and dysmorphic features. Neuroblastoma did not develop in any of these cases (Jennings et al., 2012).


Paired-like homeodomain proteins Phox2a/Arix and Phox2b/NBPhox have similar genetic organization and independently regulate dopamine beta-hydroxylase gene transcription.
Adachi M, Browne D, Lewis EJ.
DNA Cell Biol. 2000 Sep;19(9):539-54.
PMID 11034547
Polyalanine expansion and frameshift mutations of the paired-like homeobox gene PHOX2B in congenital central hypoventilation syndrome.
Amiel J, Laudier B, Attie-Bitach T, Trang H, de Pontual L, Gener B, Trochet D, Etchevers H, Ray P, Simonneau M, Vekemans M, Munnich A, Gaultier C, Lyonnet S.
Nat Genet. 2003 Apr;33(4):459-61. Epub 2003 Mar 17.
PMID 12640453
Recurrence of CCHS associated PHOX2B poly-alanine expansion mutation due to maternal mosaicism.
Bachetti T, Di Duca M, Monica MD, Grappone L, Scarano G, Ceccherini I.
Pediatr Pulmonol. 2013 Mar 4. doi: 10.1002/ppul.22790. [Epub ahead of print]
PMID 23460545
PMX2B, a new candidate gene for Hirschsprung's disease.
Benailly HK, Lapierre JM, Laudier B, Amiel J, Attie T, De Blois MC, Vekemans M, Romana SP.
Clin Genet. 2003 Sep;64(3):204-9.
PMID 12919134
The TLX2 homeobox gene is a transcriptional target of PHOX2B in neural-crest-derived cells.
Borghini S, Bachetti T, Fava M, Di Duca M, Cargnin F, Fornasari D, Ravazzolo R, Ceccherini I.
Biochem J. 2006 Apr 15;395(2):355-61.
PMID 16402914
Phox2 genes - from patterning to connectivity.
Brunet JF, Pattyn A.
Curr Opin Genet Dev. 2002 Aug;12(4):435-40. (REVIEW)
PMID 12100889
PHOX2B regulates its own expression by a transcriptional auto-regulatory mechanism.
Cargnin F, Flora A, Di Lascio S, Battaglioli E, Longhi R, Clementi F, Fornasari D.
J Biol Chem. 2005 Nov 11;280(45):37439-48. Epub 2005 Sep 6.
PMID 16144830
Homeoprotein Phox2b commands a somatic-to-visceral switch in cranial sensory pathways.
D'Autreaux F, Coppola E, Hirsch MR, Birchmeier C, Brunet JF.
Proc Natl Acad Sci U S A. 2011 Dec 13;108(50):20018-23. doi: 10.1073/pnas.1110416108. Epub 2011 Nov 29.
PMID 22128334
The role of Phox2b in synchronizing pan-neuronal and type-specific aspects of neurogenesis.
Dubreuil V, Hirsch MR, Jouve C, Brunet JF, Goridis C.
Development. 2002 Nov;129(22):5241-53.
PMID 12399315
Contributions of PHOX2B in the pathogenesis of Hirschsprung disease.
Fernandez RM, Mathieu Y, Luzon-Toro B, Nunez-Torres R, Gonzalez-Meneses A, Antinolo G, Amiel J, Borrego S.
PLoS One. 2013;8(1):e54043. doi: 10.1371/journal.pone.0054043. Epub 2013 Jan 14.
PMID 23342068
Sp proteins and Phox2b regulate the expression of the human Phox2a gene.
Flora A, Lucchetti H, Benfante R, Goridis C, Clementi F, Fornasari D.
J Neurosci. 2001 Sep 15;21(18):7037-45.
PMID 11549713
Interaction of Hand2 and E2a is important for transcription of Phox2b in sympathetic nervous system neuron differentiation.
Hashimoto Y, Tsutsumi M, Myojin R, Maruta K, Onoda F, Tashiro F, Ohtsu M, Murakami Y.
Biochem Biophys Res Commun. 2011 Apr 29;408(1):38-44. doi: 10.1016/j.bbrc.2011.03.113. Epub 2011 Mar 29.
PMID 21453680
Trim11 increases expression of dopamine beta-hydroxylase gene by interacting with Phox2b.
Hong SJ, Chae H, Lardaro T, Hong S, Kim KS.
Biochem Biophys Res Commun. 2008 Apr 11;368(3):650-5. doi: 10.1016/j.bbrc.2008.01.165. Epub 2008 Feb 12.
PMID 18275850
Variable human phenotype associated with novel deletions of the PHOX2B gene.
Jennings LJ, Yu M, Rand CM, Kravis N, Berry-Kravis EM, Patwari PP, Weese-Mayer DE.
Pediatr Pulmonol. 2012 Feb;47(2):153-61. doi: 10.1002/ppul.21527. Epub 2011 Aug 9.
PMID 21830319
Central nervous system distribution of the transcription factor Phox2b in the adult rat.
Kang BJ, Chang DA, Mackay DD, West GH, Moreira TS, Takakura AC, Gwilt JM, Guyenet PG, Stornetta RL.
J Comp Neurol. 2007 Aug 10;503(5):627-41.
PMID 17559094
Specification of neurotransmitter identity by Phox2 proteins in neural crest stem cells.
Lo L, Morin X, Brunet JF, Anderson DJ.
Neuron. 1999 Apr;22(4):693-705.
PMID 10230790
PHOX2A and PHOX2B genes are highly co-expressed in human neuroblastoma.
Longo L, Borghini S, Schena F, Parodi S, Albino D, Bachetti T, Da Prato L, Truini M, Gambini C, Tonini GP, Ceccherini I, Perri P.
Int J Oncol. 2008 Nov;33(5):985-91.
PMID 18949361
PHOX2B mutations and polyalanine expansions correlate with the severity of the respiratory phenotype and associated symptoms in both congenital and late onset Central Hypoventilation syndrome.
Matera I, Bachetti T, Puppo F, Di Duca M, Morandi F, Casiraghi GM, Cilio MR, Hennekam R, Hofstra R, Schober JG, Ravazzolo R, Ottonello G, Ceccherini I.
J Med Genet. 2004 May;41(5):373-80.
PMID 15121777
PHOX2B analysis in non-syndromic neuroblastoma cases shows novel mutations and genotype-phenotype associations.
McConville C, Reid S, Baskcomb L, Douglas J, Rahman N.
Am J Med Genet A. 2006 Jun 15;140(12):1297-301.
PMID 16691592
Inheritance of polyalanine expansion mutation of PHOX2B in congenital central hypoventilation syndrome.
Meguro T, Yoshida Y, Hayashi M, Toyota K, Otagiri T, Mochizuki N, Kishikawa Y, Sasaki A, Hayasaka K.
J Hum Genet. 2012 May;57(5):335-7. doi: 10.1038/jhg.2012.27. Epub 2012 Mar 22.
PMID 22437207
Germline PHOX2B mutation in hereditary neuroblastoma.
Mosse YP, Laudenslager M, Khazi D, Carlisle AJ, Winter CL, Rappaport E, Maris JM.
Am J Hum Genet. 2004 Oct;75(4):727-30.
PMID 15338462
Autonomic neurocristopathy-associated mutations in PHOX2B dysregulate Sox10 expression.
Nagashimada M, Ohta H, Li C, Nakao K, Uesaka T, Brunet JF, Amiel J, Trochet D, Wakayama T, Enomoto H.
J Clin Invest. 2012 Sep 4;122(9):3145-58. doi: 10.1172/JCI63401. Epub 2012 Aug 27.
PMID 22922260
Parental origin and somatic mosaicism of PHOX2B mutations in Congenital Central Hypoventilation Syndrome.
Parodi S, Bachetti T, Lantieri F, Di Duca M, Santamaria G, Ottonello G, Matera I, Ravazzolo R, Ceccherini I.
Hum Mutat. 2008 Jan;29(1):206.
PMID 18157832
Control of hindbrain motor neuron differentiation by the homeobox gene Phox2b.
Pattyn A, Hirsch M, Goridis C, Brunet JF.
Development. 2000 Apr;127(7):1349-58.
PMID 10704382
The homeobox gene Phox2b is essential for the development of autonomic neural crest derivatives.
Pattyn A, Morin X, Cremer H, Goridis C, Brunet JF.
Nature. 1999 May 27;399(6734):366-70.
PMID 10360575
Prevalence and functional consequence of PHOX2B mutations in neuroblastoma.
Raabe EH, Laudenslager M, Winter C, Wasserman N, Cole K, LaQuaglia M, Maris DJ, Mosse YP, Maris JM.
Oncogene. 2008 Jan 17;27(4):469-76. Epub 2007 Jul 16.
PMID 17637745
The MSX1 homeobox transcription factor is a downstream target of PHOX2B and activates the Delta-Notch pathway in neuroblastoma.
Revet I, Huizenga G, Chan A, Koster J, Volckmann R, van Sluis P, Ora I, Versteeg R, Geerts D.
Exp Cell Res. 2008 Feb 15;314(4):707-19. doi: 10.1016/j.yexcr.2007.12.008. Epub 2008 Jan 16.
PMID 18201699
Integration of anteroposterior and dorsoventral regulation of Phox2b transcription in cranial motoneuron progenitors by homeodomain proteins.
Samad OA, Geisen MJ, Caronia G, Varlet I, Zappavigna V, Ericson J, Goridis C, Rijli FM.
Development. 2004 Aug;131(16):4071-83.
PMID 15289435
Molecular analysis of congenital central hypoventilation syndrome.
Sasaki A, Kanai M, Kijima K, Akaba K, Hashimoto M, Hasegawa H, Otaki S, Koizumi T, Kusuda S, Ogawa Y, Tuchiya K, Yamamoto W, Nakamura T, Hayasaka K.
Hum Genet. 2003 Dec;114(1):22-6. Epub 2003 Oct 18.
PMID 14566559
Expression of Phox2b by brainstem neurons involved in chemosensory integration in the adult rat.
Stornetta RL, Moreira TS, Takakura AC, Kang BJ, Chang DA, West GH, Brunet JF, Mulkey DK, Bayliss DA, Guyenet PG.
J Neurosci. 2006 Oct 4;26(40):10305-14.
PMID 17021186
Association between schizophrenia with ocular misalignment and polyalanine length variation in PMX2B.
Toyota T, Yoshitsugu K, Ebihara M, Yamada K, Ohba H, Fukasawa M, Minabe Y, Nakamura K, Sekine Y, Takei N, Suzuki K, Itokawa M, Meerabux JM, Iwayama-Shigeno Y, Tomaru Y, Shimizu H, Hattori E, Mori N, Yoshikawa T.
Hum Mol Genet. 2004 Mar 1;13(5):551-61. Epub 2004 Jan 6.
PMID 14709596
In Vitro studies of non poly alanine PHOX2B mutations argue against a loss-of-function mechanism for congenital central hypoventilation.
Trochet D, Mathieu Y, Pontual Ld, Savarirayan R, Munnich A, Brunet JF, Lyonnet S, Goridis C, Amiel J.
Hum Mutat. 2009 Feb;30(2):E421-31. doi: 10.1002/humu.20923.
PMID 19058226
PHOX2B genotype allows for prediction of tumor risk in congenital central hypoventilation syndrome.
Trochet D, O'Brien LM, Gozal D, Trang H, Nordenskjold A, Laudier B, Svensson PJ, Uhrig S, Cole T, Niemann S, Munnich A, Gaultier C, Lyonnet S, Amiel J.
Am J Hum Genet. 2005 Mar;76(3):421-6. Epub 2005 Jan 18.
PMID 15657873
PHOX2B germline and somatic mutations in late-onset central hypoventilation syndrome.
Trochet D, de Pontual L, Straus C, Gozal D, Trang H, Landrieu P, Munnich A, Lyonnet S, Gaultier C, Amiel J.
Am J Respir Crit Care Med. 2008b Apr 15;177(8):906-11. Epub 2007 Dec 13.
PMID 18079495
A Phox2- and Hand2-dependent Hand1 cis-regulatory element reveals a unique gene dosage requirement for Hand2 during sympathetic neurogenesis.
Vincentz JW, VanDusen NJ, Fleming AB, Rubart M, Firulli BA, Howard MJ, Firulli AB.
J Neurosci. 2012 Feb 8;32(6):2110-20. doi: 10.1523/JNEUROSCI.3584-11.2012.
PMID 22323723
An official ATS clinical policy statement: Congenital central hypoventilation syndrome: genetic basis, diagnosis, and management.
Weese-Mayer DE, Berry-Kravis EM, Ceccherini I, Keens TG, Loghmanee DA, Trang H; ATS Congenital Central Hypoventilation Syndrome Subcommittee.
Am J Respir Crit Care Med. 2010 Mar 15;181(6):626-44. doi: 10.1164/rccm.200807-1069ST.
PMID 20208042
An ancestral variant of Secretogranin II confers regulation by PHOX2 transcription factors and association with hypertension.
Wen G, Wessel J, Zhou W, Ehret GB, Rao F, Stridsberg M, Mahata SK, Gent PM, Das M, Cooper RS, Chakravarti A, Zhou H, Schork NJ, O'connor DT, Hamilton BA.
Hum Mol Genet. 2007 Jul 15;16(14):1752-64. Epub 2007 Jun 21.
PMID 17584765
Interaction between PHOX2B and CREBBP mediates synergistic activation: mechanistic implications of PHOX2B mutants.
Wu HT, Su YN, Hung CC, Hsieh WS, Wu KJ.
Hum Mutat. 2009 Apr;30(4):655-60. doi: 10.1002/humu.20929.
PMID 19191321
Methylation-associated PHOX2B gene silencing is a rare event in human neuroblastoma.
de Pontual L, Trochet D, Bourdeaut F, Thomas S, Etchevers H, Chompret A, Minard V, Valteau D, Brugieres L, Munnich A, Delattre O, Lyonnet S, Janoueix-Lerosey I, Amiel J.
Eur J Cancer. 2007 Nov;43(16):2366-72. Epub 2007 Aug 31.
PMID 17765533
The Phox2B homeobox gene is mutated in sporadic neuroblastomas.
van Limpt V, Schramm A, van Lakeman A, Sluis P, Chan A, van Noesel M, Baas F, Caron H, Eggert A, Versteeg R.
Oncogene. 2004 Dec 9;23(57):9280-8.
PMID 15516980


This paper should be referenced as such :
Bachetti, T ; Ceccherini, I
PHOX2B (paired-like homeobox 2b)
Atlas Genet Cytogenet Oncol Haematol. 2013;17(11):740-745.
Free journal version : [ pdf ]   [ DOI ]
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Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 1 ]
  Nervous system: Peripheral neuroblastic tumours (Neuroblastoma, Ganglioneuroblastoma, Ganglioneuroma)

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