EuRBPDB

Note: to get the extension of tumor abbreviations.

Cancer Related Information
Basic Information

Cancer associated literatures

PID	Title	Article	Time	Author	Doi
15753651	Cdk9 regulates neural differentiation and its expression correlates with the differentiation grade of neuroblastoma and PNET tumors.	Cancer Biol Ther	2005 Mar	De Falco G	-
28940993	miR-206 inhibits the growth of hepatocellular carcinoma cells via targeting CDK9.	Cancer Med	2017 Oct	Pang C	doi: 10.1002/cam4.1188
25281924	MicroRNA-874 inhibits cell proliferation and induces apoptosis in human breast cancer by targeting CDK9.	FEBS Lett	2014 Dec 20	Wang L	doi: 10.1016/j.febslet.2014.09.035
24688048	A novel CDK9 inhibitor shows potent antitumor efficacy in preclinical hematologic tumor models.	Mol Cancer Ther	2014 Jun	Yin T	doi: 10.1158/1535-7163.MCT-13-0849
20980437	CDK9 regulates AR promoter selectivity and cell growth through serine 81 phosphorylation.	Mol Endocrinol	2010 Dec	Gordon V	doi: 10.1210/me.2010-0238
17998334	Parvin-beta inhibits breast cancer tumorigenicity and promotes CDK9-mediated peroxisome proliferator-activated receptor gamma 1 phosphorylation.	Mol Cell Biol	2008 Jan	Johnstone CN	-
22391209	Flavopiridol induces phosphorylation of AKT in a human glioblastoma cell line, in contrast to siRNA-mediated silencing of Cdk9: Implications for drug design and development.	Cell Cycle	2012 Mar 15	Caracciolo V	doi: 10.4161/cc.11.6.19663
27486754	Inhibition of cyclin dependent kinase 9 by dinaciclib suppresses cyclin B1 expression and tumor growth in triple negative breast cancer.	Oncotarget	2016 Aug 30	Rajput S	doi: 10.18632/oncotarget.10870.
28722178	CDK9: A key player in cancer and other diseases.	J Cell Biochem	2018 Feb	Franco LC	doi: 10.1002/jcb.26293
28701053	MicroRNA-613 inhibits the progression of gastric cancer by targeting CDK9.	Artif Cells Nanomed Biotechnol	2018 Aug	Lu Y	doi: 10.1080/21691401.2017.1351983

Expression in 33 cancers

Mutations

Cancer	Chr	Position	Mutation Type	dbSNP	Protein-change	Allele Freq
BLCA	chr9	127788216	Splice_Region	novel	I145I	0.38
BLCA	chr9	127787600	Missense_Mutation	rs371317161	R86Q	0.34
BLCA	chr9	127787600	Missense_Mutation	rs371317161	R86Q	0.32
BLCA	chr9	127789376	Missense_Mutation	novel	D318N	0.72
BLCA	chr9	127786771	Missense_Mutation	novel	E55Q	0.67
BLCA	chr9	127788278	Missense_Mutation	novel	A166V	0.58
BLCA	chr9	127787586	Missense_Mutation	novel	L81F	0.13
BLCA	chr9	127789529	Missense_Mutation	novel	E369Q	0.09
BRCA	chr9	127789698	3'UTR	novel		0.33
BRCA	chr9	127788017	Silent	NA	G112G	0.15
CESC	chr9	127789621	3'UTR	novel		0.1
COAD	chr9	127789217	Missense_Mutation	NA	L265V	0.19
COAD	chr9	127789205	Silent	NA	L261L	0.45
COAD	chr9	127788385	Missense_Mutation	rs770506343	G202R	0.26
COAD	chr9	127789275	Missense_Mutation	NA	R284H	0.4
COAD	chr9	127789274	Missense_Mutation	rs370938433	R284C	0.46
COAD	chr9	127789423	Silent	rs150060991	T333T	0.23
GBM	chr9	127789451	Missense_Mutation	novel	R343S	0.06
GBM	chr9	127789452	Frame_Shift_Del	novel	*R343Pfs48**	0.23
GBM	chr9	127787541	Silent	novel	E66E	0.45
HNSC	chr9	127788654	Missense_Mutation	rs11554104	A239T	0.26
HNSC	chr9	127789253	Missense_Mutation	novel	D277N	0.27
HNSC	chr9	127786238	Missense_Mutation	novel	F30L	0.16
LIHC	chr9	127789248	Missense_Mutation	novel	V275A	0.42
LIHC	chr9	127789547	3'UTR	novel		0.39
LIHC	chr9	127788664	Missense_Mutation	NA	S242I	0.74
LIHC	chr9	127789344	Missense_Mutation	NA	D307V	0.46
LIHC	chr9	127788664	Missense_Mutation	NA	S242I	0.24
LIHC	chr9	127788230	Missense_Mutation	novel	M150T	0.35
LUAD	chr9	127788300	Silent	NA	A173A	0.23
LUAD	chr9	127788381	Missense_Mutation	novel	L200F	0.32
LUAD	chr9	127789338	Missense_Mutation	NA	D305A	0.21
LUAD	chr9	127789249	Silent	NA	V275V	0.08
LUAD	chr9	127789545	3'UTR	novel		0.12
MESO	chr9	127786093	5'UTR	novel		0.26
OV	chr9	127789212	Missense_Mutation	novel	E263A	0.18
OV	chr9	127789279	Silent	novel	D285D	0.14
PAAD	chr9	127789331	Missense_Mutation	NA	R303C	0.24
READ	chr9	127789301	Missense_Mutation	NA	D293Y	0.32
READ	chr9	127789497	Missense_Mutation	rs753758776	R358H	0.17
SKCM	chr9	127787521	Missense_Mutation	NA	P60S	0.18
SKCM	chr9	127788369	Silent	NA	P196P	0.25
SKCM	chr9	127788284	Missense_Mutation	NA	F168S	0.12
SKCM	chr9	127787990	Silent	rs573934552	F103F	0.81
SKCM	chr9	127789426	Silent	rs142704308	S334S	0.41
SKCM	chr9	127789346	Missense_Mutation	novel	D308Y	0.63
STAD	chr9	127789427	Missense_Mutation	NA	M335V	0.36
STAD	chr9	127786119	5'UTR	novel		0.23
STAD	chr9	127788274	Missense_Mutation	NA	L165M	0.11
STAD	chr9	127789533	Missense_Mutation	NA	R370H	0.07
THCA	chr9	127788235	Missense_Mutation	novel	A152S	0.13
UCEC	chr9	127789700	3'UTR	novel		0.55
UCEC	chr9	127789241	Missense_Mutation	rs376244572	R273W	0.49
UCEC	chr9	127786173	Missense_Mutation	novel	E9K	0.18
UCEC	chr9	127788371	Missense_Mutation	novel	P197L	0.8
UCEC	chr9	127789987	3'UTR	novel		0.12
UCEC	chr9	127787536	Missense_Mutation	novel	R65W	0.35
UCEC	chr9	127789480	Missense_Mutation	novel	Q352H	0.16
UCEC	chr9	127789746	3'UTR	novel		0.2
UCEC	chr9	127788597	Missense_Mutation	novel	A220T	0.3
UCEC	chr9	127789699	3'UTR	novel		0.29
UCEC	chr9	127789832	3'UTR	novel		0.27
UCEC	chr9	127789547	3'UTR	novel		0.34
UCEC	chr9	127789832	3'UTR	novel		0.31
UCEC	chr9	127789331	Missense_Mutation	NA	R303C	0.33
UCEC	chr9	127788046	Missense_Mutation	novel	T122M	0.33
UCEC	chr9	127788216	Splice_Region	novel	I145I	0.56
UCEC	chr9	127788032	Silent	novel	V117V	0.44
UCEC	chr9	127788559	Frame_Shift_Ins	rs755440676	*I210Hfs2**	0.47
UCEC	chr9	127787600	Missense_Mutation	rs371317161	R86Q	0.39
UCEC	chr9	127789348	Silent	rs201136315	D308D	0.38
UCEC	chr9	127787962	Missense_Mutation	NA	R94H	0.43
UCEC	chr9	127789438	Silent	novel	Y338Y	0.32
UCEC	chr9	127789342	Silent	rs141597514	S306S	0.21
UCEC	chr9	127789300	Silent	rs574082027	I292I	0.35
UCEC	chr9	127789552	3'UTR	rs377000414		0.36

Copy Number Variations (CNVs)

Cancer	Type	Freq	Q-value
CHOL	DEL	0.4167	0.067545
LAML	DEL	0.0052	0.24147
LGG	AMP	0.0585	0.21332
LIHC	DEL	0.2459	0.12467
PRAD	AMP	0.0833	0.059049
THCA	DEL	0.0401	0.24038
THYM	DEL	0.0163	0.022012
UCS	DEL	0.5536	0.089783

Survival Analysis

Cancer	P-value	Q-value
THYM	0.0037	Kaplan-Meier Survival Analysis
KIRC	0.00011	Kaplan-Meier Survival Analysis
SARC	0.00097	Kaplan-Meier Survival Analysis
MESO	0.05	Kaplan-Meier Survival Analysis
ACC	0.017	Kaplan-Meier Survival Analysis
LUSC	0.018	Kaplan-Meier Survival Analysis
ESCA	0.0014	Kaplan-Meier Survival Analysis
COAD	0.0014	Kaplan-Meier Survival Analysis
PAAD	0.00067	Kaplan-Meier Survival Analysis
BLCA	0.016	Kaplan-Meier Survival Analysis
READ	0.027	Kaplan-Meier Survival Analysis
LAML	0.017	Kaplan-Meier Survival Analysis
UCEC	0.034	Kaplan-Meier Survival Analysis
THCA	0.027	Kaplan-Meier Survival Analysis
UVM	0.018	Kaplan-Meier Survival Analysis
OV	0.01	Kaplan-Meier Survival Analysis

Drugs

Cell lines and drugs in GSE70138 or GSE92742

Description

RBPome

Literatures

Expression

Transcripts

Gene Model

Pathway

PPI

Gene Ontology

Description

Ensembl ID: ENSG00000136807 (Gene tree)
Gene ID: 1025
Gene Symbol: CDK9
Alias: PITALRE|C-2k|TAK|CDC2L4
Full Name: cyclin dependent kinase 9
Gene Type: protein_coding
Specie: Homo_sapiens
Strand: Plus strand
Length: 5,109 bases
Position: chr9:127,785,679-127,790,787
Accession: 1780
Summary: The protein encoded by this gene is a member of the cyclin-dependent protein kinase (CDK) family. CDK family members are highly similar to the gene products of S. cerevisiae cdc28, and S. pombe cdc2, and known as important cell cycle regulators. This kinase was found to be a component of the multiprotein complex TAK/P-TEFb, which is an elongation factor for RNA polymerase II-directed transcription and functions by phosphorylating the C-terminal domain of the largest subunit of RNA polymerase II. This protein forms a complex with and is regulated by its regulatory subunit cyclin T or cyclin K. HIV-1 Tat protein was found to interact with this protein and cyclin T, which suggested a possible involvement of this protein in AIDS. [provided by RefSeq, Jul 2008]

RNA binding proteome (RBPome)

PID	Title	Method	Time	Author	Doi
30607034	Comprehensive identification of RNA protein interactions in any organism using orthogonal organic phase separation (OOPS)	OOPS & HEK293	2019 Jan 3	Queiroz RML	DOI: 10.1038/s41587-018-0001-2
30528433	The Human RNA-Binding Proteome and Its Dynamics during Translational Arrest	XRNAX & HEK293	2018 Dec 6	Trendel J	DOI: 10.1016/j.cell.2018.11.004
30528433	The Human RNA-Binding Proteome and Its Dynamics during Translational Arrest	XRNAX & Hela	2018 Dec 6	Trendel J	DOI: 10.1016/j.cell.2018.11.004
30607034	Comprehensive identification of RNA protein interactions in any organism using orthogonal organic phase separation (OOPS)	OOPS & MCF10A	2019 Jan 3	Queiroz RML	DOI: 10.1038/s41587-018-0001-2
30528433	The Human RNA-Binding Proteome and Its Dynamics during Translational Arrest	XRNAX & MCF7	2018 Dec 6	Trendel J	DOI: 10.1016/j.cell.2018.11.004
30607034	Comprehensive identification of RNA protein interactions in any organism using orthogonal organic phase separation (OOPS)	OOPS & U2OS	2019 Jan 3	Queiroz RML	DOI: 10.1038/s41587-018-0001-2

Literatures on RNA binding capacity

PID	Title	Article	Time	Author	Doi
29563491	RNA cytosine methylation and methyltransferases mediate chromatin organization and 5-azacytidine response and resistance in leukaemia.	Nat Commun	2018 Mar 21	Cheng JX	doi: 10.1038/s41467-018-03513-4.
14585207	Additive activity between the trans-activation response RNA-binding protein, TRBP2, and cyclin T1 on HIV type 1 expression and viral production in murine cells.	AIDS Res Hum Retroviruses	2003 Sep	Battisti PL	-
19941902	High yield expression and purification of HIV-1 Tat1-72 for structural studies.	J Virol Methods	2010 Mar	Shojania S	doi: 10.1016/j.jviromet.2009.11.021
30637779	Long-Read RNA Sequencing Identifies Alternative Splice Variants in Hepatocellular Carcinoma and Tumor-Specific Isoforms.	Hepatology	2019 Jan 13	Chen H	doi: 10.1002/hep.30500
16280076	light on transcription initiation.	Retrovirology	2005 Nov 9	Brady J	-
15677471	The STAT3 transcription factor is a target for the Myc and riboblastoma proteins on the Cdc25A promoter.	J Biol Chem	2005 Apr 22	Barre B	-
10545121	HIV-1 tat transcriptional activity is regulated by acetylation.	EMBO J	1999 Nov 1	Kiernan RE	-
10550206	Tackling Tat.	J Mol Biol	1999 Oct 22	Karn J	-
10082552	Tat activates human immunodeficiency virus type 1 transcriptional elongation independent of TFIIH kinase.	Mol Cell Biol	1999 Apr	Chen D	-
9491887	A novel CDK9-associated C-type cyclin interacts directly with HIV-1 Tat and mediates its high-affinity, loop-specific binding to TAR RNA.	Cell	1998 Feb 20	Wei P	-
10467404	Transcriptional regulation by targeted recruitment of cyclin-dependent CDK9 kinase in vivo.	Oncogene	1999 Aug 12	Majello B	-
12438622	RNA interference directed against viral and cellular targets inhibits human immunodeficiency Virus Type 1 replication.	J Virol	2002 Dec	Surabhi RM	-
11572868	TFIIH inhibits CDK9 phosphorylation during human immunodeficiency virus type 1 transcription.	J Biol Chem	2001 Nov 30	Zhou M	-
10958691	CDK9 autophosphorylation regulates high-affinity binding of the human immunodeficiency virus type 1 tat-P-TEFb complex to TAR RNA.	Mol Cell Biol	2000 Sep	Garber ME	-
15528190	Cyclin-dependent kinase 9 is required for tumor necrosis factor-alpha-stimulated matrix metalloproteinase-9 expression in human lung adenocarcinoma cells.	J Biol Chem	2005 Jan 14	Shan B	-
19136461	Binding to DNA of the RNA-polymerase II C-terminal domain allows discrimination between Cdk7 and Cdk9 phosphorylation.	Nucleic Acids Res	2009 Mar	Lolli G	doi: 10.1093/nar/gkn1061
18223296	The bromodomain protein Brd4 stimulates G1 gene transcription and promotes progression to S phase.	J Biol Chem	2008 Apr 4	Mochizuki K	doi: 10.1074/jbc.M707603200
17956865	The functional role of an interleukin 6-inducible CDK9.STAT3 complex in human gamma-fibrinogen gene expression.	J Biol Chem	2007 Dec 21	Hou T	-
22113271	Two-step cross-linking for analysis of protein-chromatin interactions.	Methods Mol Biol	2012	Tian B	doi: 10.1007/978-1-61779-376-9_7.
21900162	RelA Ser276 phosphorylation-coupled Lys310 acetylation controls transcriptional elongation of inflammatory cytokines in respiratory syncytial virus infection.	J Virol	2011 Nov	Brasier AR	doi: 10.1128/JVI.05360-11
21763498	Reciprocal regulation of human immunodeficiency virus-1 gene expression and replication by heat shock proteins 40 and 70.	J Mol Biol	2011 Jul 29	Kumar M	doi: 10.1016/j.jmb.2011.04.005.
24985467	A single point mutation in cyclin T1 eliminates binding to Hexim1, Cdk9 and RNA but not to AFF4 and enforces repression of HIV transcription.	Retrovirology	2014 Jul 1	Kuzmina A	doi: 10.1186/1742-4690-11-51.
28077651	BRD4 Couples NF-kB/RelA with Airway Inflammation and the IRF-RIG-I Amplification Loop in Respiratory Syncytial Virus Infection.	J Virol	2017 Feb 28	Tian B	doi: 10.1128/JVI.00007-17
28940993	miR-206 inhibits the growth of hepatocellular carcinoma cells via targeting CDK9.	Cancer Med	2017 Oct	Pang C	doi: 10.1002/cam4.1188
29792216	HIV-1 Tat phosphorylation on Ser-16 residue modulates HIV-1 transcription.	Retrovirology	2018 May 23	Ivanov A	doi: 10.1186/s12977-018-0422-5.

Expression

Transcripts

Transcript ID	Name	Length	RefSeq ID	Protein ID	Length	RefSeq ID	UniportKB ID
ENST00000373264	CDK9-201	2463	-	ENSP00000362361	372 (aa)	-	P50750
ENST00000480353	CDK9-203	706	-	-	- (aa)	-	-
ENST00000498339	CDK9-205	458	-	-	- (aa)	-	-
ENST00000421939	CDK9-202	702	-	ENSP00000395872	194 (aa)	-	X6RE90
ENST00000491521	CDK9-204	510	-	-	- (aa)	-	-

Gene Model

Click here to download 's gene model file

Pathway

Pathway ID	Pathway Name	Source
hsa05202	Transcriptional misregulation in cancer	KEGG

Protein-Protein Interaction (PPI)

Clik here to download ENSG00000136807's network

Gene Ontology

Go ID	Go_term	PubmedID	Evidence	Category
GO:0000307	cyclin-dependent protein kinase holoenzyme complex	21873635.	IBA	Component
GO:0000790	nuclear chromatin	21873635.	IBA	Component
GO:0000978	RNA polymerase II proximal promoter sequence-specific DNA binding	-	IEA	Function
GO:0001223	transcription coactivator binding	12037672.	IPI	Function
GO:0003677	DNA binding	16109376.	IDA	Function
GO:0003682	chromatin binding	-	ISS	Function
GO:0004672	protein kinase activity	8170997.	TAS	Function
GO:0004674	protein serine/threonine kinase activity	-	TAS	Function
GO:0004693	cyclin-dependent protein serine/threonine kinase activity	21873635.	IBA	Function
GO:0004693	cyclin-dependent protein serine/threonine kinase activity	12037670.	IDA	Function
GO:0005515	protein binding	9499409.12832472.14580347.15107825.15286705.15563843.15713662.16331689.17690245.18281698.18483487.18566585.19387490.19914168.20153263.20535204.20562857.20930849.21533037.21729782.22190034.22939624.22959624.23455922.23602568.24189400.24360279.25036637.25470060.26659056.28330616.	IPI	Function
GO:0005524	ATP binding	-	IEA	Function
GO:0005634	nucleus	21873635.	IBA	Component
GO:0005654	nucleoplasm	-	IDA	Component
GO:0005654	nucleoplasm	-	TAS	Component
GO:0005694	chromosome	21873635.	IBA	Component
GO:0006281	DNA repair	-	IEA	Process
GO:0006282	regulation of DNA repair	20493174.	IDA	Process
GO:0006366	transcription by RNA polymerase II	-	TAS	Process
GO:0006367	transcription initiation from RNA polymerase II promoter	10866664.	TAS	Process
GO:0006368	transcription elongation from RNA polymerase II promoter	21873635.	IBA	Process
GO:0006368	transcription elongation from RNA polymerase II promoter	-	TAS	Process
GO:0006468	protein phosphorylation	21873635.	IBA	Process
GO:0006468	protein phosphorylation	16109376.	IDA	Process
GO:0007346	regulation of mitotic cell cycle	19575011.	IMP	Process
GO:0008023	transcription elongation factor complex	22195968.	IDA	Component
GO:0008024	cyclin/CDK positive transcription elongation factor complex	21873635.	IBA	Component
GO:0008024	cyclin/CDK positive transcription elongation factor complex	9499409.15905409.	IDA	Component
GO:0008134	transcription factor binding	21873635.	IBA	Function
GO:0008283	cell proliferation	8170997.	TAS	Process
GO:0008353	RNA polymerase II CTD heptapeptide repeat kinase activity	21873635.	IBA	Function
GO:0008353	RNA polymerase II CTD heptapeptide repeat kinase activity	9499409.12721286.	IDA	Function
GO:0010613	positive regulation of cardiac muscle hypertrophy	-	IEA	Process
GO:0016020	membrane	19946888.	HDA	Component
GO:0016301	kinase activity	-	TAS	Function
GO:0016605	PML body	18250157.	IDA	Component
GO:0019901	protein kinase binding	-	IEA	Function
GO:0030332	cyclin binding	21873635.	IBA	Function
GO:0031056	regulation of histone modification	19844166.	IDA	Process
GO:0031297	replication fork processing	20930849.	IDA	Process
GO:0032968	positive regulation of transcription elongation from RNA polymerase II promoter	21873635.	IBA	Process
GO:0033129	positive regulation of histone phosphorylation	19575011.	IMP	Process
GO:0036464	cytoplasmic ribonucleoprotein granule	-	IDA	Component
GO:0042493	response to drug	-	IEA	Process
GO:0042795	snRNA transcription by RNA polymerase II	-	TAS	Process
GO:0044212	transcription regulatory region DNA binding	21873635.	IBA	Function
GO:0045944	positive regulation of transcription by RNA polymerase II	21873635.	IBA	Process
GO:0045944	positive regulation of transcription by RNA polymerase II	19575011.	IMP	Process
GO:0045944	positive regulation of transcription by RNA polymerase II	-	TAS	Process
GO:0050434	positive regulation of viral transcription	-	TAS	Process
GO:0051147	regulation of muscle cell differentiation	12037670.	IMP	Process
GO:0070816	phosphorylation of RNA polymerase II C-terminal domain	21873635.	IBA	Process
GO:0071157	negative regulation of cell cycle arrest	20930849.	IDA	Process
GO:0071345	cellular response to cytokine stimulus	17956865.	IDA	Process
GO:0097322	7SK snRNA binding	11713533.	IDA	Function
GO:1900364	negative regulation of mRNA polyadenylation	19575011.	IMP	Process
GO:1903839	positive regulation of mRNA 3'-UTR binding	19575011.	IDA	Process
GO:2001168	positive regulation of histone H2B ubiquitination	19575011.	IMP	Process

EuRBPDB

Note: to get the extension of tumor abbreviations.

Select Dataset :

Input Drug :

Input Cell Line :

Eesembl ID

Cell lines and drugs in GSE70138 or GSE92742

Description

RBPome

Literatures

Expression

Transcripts

Gene Model

Pathway

PPI

Gene Ontology

Note: Click here to get the extension of tumor abbreviations.

Select Dataset :

Input Drug :

Input Cell Line :

Eesembl ID

Cell lines and drugs in GSE70138 or GSE92742

Note: to get the extension of tumor abbreviations.