© 2016 Roychoudhuri Lab. Site hosted on Github and run on Jekyll. About the website.
Most tools for analysing large gene expression datasets, including The Cancer Genome Atlas (TCGA), focus on analysis of expression of individual genes or inference of the abundance of specific cell types from global gene expression data. While these methods provide useful insights, they can overlook crucial process-based information that could enhance our understanding of cancer biology.
GS-TCGA is a resource designed to enable novel biological insights through gene set-based analyses of data from The Cancer Genome Atlas, leveraging gene sets from the Molecular Signatures Database (MSigDB).
It consists of four tools:
Gene Set Survival Analysis: GS-Surv allows the user to investigate how the average expression of genes in a specified gene set relates to overall survival in patient data.
Co-Correlative Gene Set Enrichment Analysis: CC-GSEA allows generation of novel hypotheses of gene function through performing GSEA on co-correlated genes.
Gene Set Correlative Analysis: GS-Corr calculates the average expression of a gene set and correlates this with individual genes.
GS-Surv (Custom): This function allows you to upload your own gene set for GS-Surv survival analysis.
GS-TCGA was created by Tarrion Baird in our lab in 2023 and can be accessed at: http://gs-tcga.roychoudhurilab.org/
We are committed to providing public access to high-quality high-content datasets generated in the laboratory. Links below provide access to deposited high-throughput sequencing datasets generated by the laboratory through our primary and collaborative work.
In various tissues, cellular
homeostasis is achieved by functionally quiescent stem cells which self renew
while giving rise to differentiated progeny. Regulatory T (Treg) cells are
composed of functionally quiescent resting Treg (rTreg) cells which
differentiate into activated Treg (aTreg) cells upon antigen stimulation. How
rTreg cells remain quiescent despite chronic exposure to cognate self- and
foreign antigens is unclear. more…
Organism: Mus musculus
Type: Expression profiling by high
throughput sequencing; Genome binding/occupancy profiling by high throughput
sequencing
Platforms: GPL13112 GPL21103 GPL17021
Download data: BED, NARROWPEAK
Accession: GSE128176;
ID: 200128176
Single-cell RNA-Seq analysis of WT and Bach2-deficient
Foxp3+ Treg cells
These are the FastQ files used for
scRNA-Seq analysis of WT and Bach2-deficient splenic Foxp3+ Treg cells
Organism: Mus musculus
Type: Expression profiling by high
throughput sequencing
Platform: GPL21103
Accession: GSE128175
ID: 200128175
Bulk RNA-Seq analysis of WT and Bach2-deficient Foxp3+
Treg cells
These are the FastQ files used for the
RNA-seq analysis of WT and Bach2-deficient splenic Foxp3+ Treg cells.
Organism: Mus musculus
Type: Expression profiling by high throughput
sequencing
Platform: GPL17021
Accession: GSE127699
ID: 200127699
Heterogeneous Bach2 expression distinguishes rTreg cells
and aTreg cells
These are the FastQ files used for
RNA-Seq analysis of splenic Foxp3+ Treg cells that express either high or low
levels of Bach2
Organism: Mus musculus
Type: Expression profiling by high throughput
sequencing
Platform: GPL17021
Accession: GSE127698
ID: 200127698
Distribution of genome-wide BACH2 or JunD binding sites
identified by ChIP-Seq in iTreg cells
In various tissues, cellular
homeostasis is achieved by functionally quiescent stem cells which selfrenew
while giving rise to differentiated progeny. Regulatory T (Treg) cells are
composed of functionally quiescent resting Treg (rTreg) cells which
differentiate into activated Treg (aTreg) cells upon antigen stimulation. How
rTreg cells remain quiescent despite chronic exposure to cognate self- and
foreign antigens is unclear. more…
Organism: Mus musculus
Type: Genome binding/occupancy profiling
by high throughput sequencing
Platform: GPL13112
Download data: BED, NARROWPEAK
Accession: GSE127695
ID: 200127695
Anti-tumor immune responses are
counteracted by CD4+ regulatory T (Treg) cells in the tumor micronenvironment,
but the molecular mechanisms responsible for the enhanced suppressive activity
of Tregs are poorly defined. High-dimensional single cell profiling of millions
of single CD4+ and CD8+ T cells from 53 chemotherapy-nave individuals with
lung adenocarcinoma identified the transcription factor IRF4 as constitutively
expressed by effector CD4+ Tregs present exclusively in tumors. more…
Organism: Homo sapiens
Type: Expression profiling by high
throughput sequencing
Platform: GPL18573
Accession: GSE128822
ID: 200128822
Much of the genetic variation
underlying susceptibility to common autoimmune and allergic diseases is
concentrated within protein non-coding regulatory elements termed
enhancers{Enhancer; Hsniz}. It has been difficult to assign functions to a
majority of enhancers that overlap immune disease-associated variants due to
their distance from the genes they regulate, our lack of understanding of the
cell types in which they operate and our inability to recapitulate the biology
of immune-mediated diseases in vitro. more…
Organism: Mus musculus
Type: Genome binding/occupancy
profiling by high throughput sequencing
Platform: GPL17021
Accession: GSE143515
ID: 200143515
Much of the genetic variation
underlying susceptibility to common autoimmune and allergic diseases is
concentrated within protein non-coding regulatory elements termed
enhancers{Enhancer; Hsniz}. It has been difficult to assign functions to a
majority of enhancers that overlap immune disease-associated variants due to
their distance from the genes they regulate, our lack of understanding of the
cell types in which they operate and our inability to recapitulate the biology
of immune-mediated diseases in vitro. more…
Organism: Mus musculus
Type: Expression profiling by high
throughput sequencing
Platform: GPL17021
Accession: GSE128198
ID: 200128198
This SuperSeries is composed of the
SubSeries listed below.
Organism: Mus musculus
Type: Expression profiling by high
throughput sequencing; Genome binding/occupancy profiling by high throughput
sequencing
Platform: GPL17021
Accession: GSE143516
ID: 200143516
Dysfunction and stemness of tumor-infiltrating T cells
are triggered by a common mechanism
The paradox of tumor immunology is that
tumor infiltrating lymphocytes (TILs) are dysfunctional in situ and yet are
capable of stem cell-like behavior with self-renewal, massive expansion,
multipotency, and eradication of large metastatic tumors. Here we report that
the overabundance of potassium in the tumor microenvironment (TME) can explain
both phenomena.
Organism: Mus musculus
Type: Genome binding/occupancy
profiling by high throughput sequencing
Accession: GSE122156
ID: 200122156
The transcription factor Myb enhances CD8+ T cell
stemness and antitumor immunity
Stem cells are maintained by
transcriptional programs promoting self-renewal and repressing differentiation.
Here, we show that the transcription factor Myb is essential for generating and
maintaining stem cells within the CD8+ T-cell memory compartment. We found
that, following viral infection, CD8+ T cells lacking Myb underwent terminal
differentiation and exhibited impaired capacity to form CD62L+ stem cell-like
memory cells. more…
Organism: Mus musculus
Type: Expression profiling by high
throughput sequencing
Platform: GPL9185
Accession: GSE112049
ID: 200112049
Different combinations of Endoglin
tissue specific enhancers define hemangioblast and hemogenic endothelium cell
fractions
Organism: Mus musculus
Type:Expression profiling by high
throughput sequencing
Platform: GPL13112
Accession: GSE77390
ID: 200077390
Ionic immune suppression within the tumour
microenvironment limits T cell effector function
Tumours progress despite being
infiltrated by effector T cells. Tumour necrosis is associated with poor
survival in a variety of cancers. Here, we report that that necrosis causes
release of an intracellular ion, potassium, into the extracellular fluid of
human and mouse tumours. Surprisingly, elevated extracellular potassium ([K+]e)
was sufficient to profoundly suppress mouse and human T cell anti-tumour
function. more…
Organism: Mus musculus
Type: Expression profiling by high
throughput sequencing
Platform: GPL17021
Accession: GSE84996
ID: 200084996
T cell oxygen-sensing proteins establish an
immunologically tolerant metastatic niche
Cancer cells must evade immune
responses at distant sites to establish metastases. The lung is a frequent site
for metastasis. We hypothesized that lung-specific immunoregulatory mechanisms
create an immunologically permissive environment for tumor colonization. We
found that T cell-intrinsic expression of the oxygen-sensing prolyl-hydroxylase
(PHD) proteins is required to maintain local tolerance against innocuous
antigens in the lung, but powerfully licenses colonization by circulating tumor
cells. more…
Organism: Mus musculus
Type: Expression profiling by high
throughput sequencing
Accession: GSE85131
ID: 200085131
The transcription factor BACH2 is required to establish
immunosuppression within tumors
Through a diversity of functional
lineages, cells of the innate and adaptive immune system either drive or
constrain immune reactions within tumors. Thus, while the immune system has a
powerful ability to recognize and kill cancer cells, this function is often
suppressed preventing clearance of disease. The transcription factor (TF) BACH2
controls the differentiation and function of multiple innate and adaptive
immune lineages, but its role in regulating tumor immunity is not known. more…
Organism: Mus musculus
Type: Expression profiling by array
Platform: GPL1261
Accession: GSE74653
ID: 200074653
BACH2 regulates CD8+ T cell differentiation by
controlling access of AP-1 factors to enhancers
T cell antigen receptor (TCR) signaling
drives distinct responses depending upon the differentiation state and context
of CD8+ T cells. We hypothesized that access of signal-dependent transcription
factors (TFs) to enhancers is dynamically regulated to shape transcriptional
responses to TCR signaling. We found that the TF BACH2 restrains terminal
differentiation to enable generation of long-lived memory cells and protective
immunity following viral infection. more…
Organism: Mus musculus
Type: Expression profiling by high
throughput sequencing; Genome binding/occupancy profiling by high throughput
sequencing
Accession: GSE77857
ID:200077857
Mitochondrial Membrane Potential Identifies Cells with
Enhanced Stemness for Cellular Therapy
Long-term survival and antitumor
immunity of adoptively transferred CD8+ T cells is dependent on their metabolic
fitness, but approaches to isolate therapeutic T cells based on metabolic
features are not well established. Here we utilized a lipophilic cationic dye
tetramethylrhodamine methyl ester (TMRM) to identify and isolate metabolically
robust T cells based on their mitochondrial membrane potential (ΔΨm). more…
Organism: Mus musculus
Type: Expression profiling by high
throughput sequencing
Platform: GPL13112
Accession: GSE74001
ID: 200074001
Gene expression data from Zeb2WT, Zeb2KO, T-betWT and
T-betKO effector CD8+ T cells during infection
ZEB2 is a multi-zinc-finger
transcription factor known to play a significant role in early neurogenesis and
in EMT-dependent tumor metastasis. While the function of ZEB2 in T lymphocytes
is unknown, activity of the closely related family member ZEB1 has been
implicated in lymphocyte development. Here, we find that ZEB2 expression is
upregulated by activated T cells, specifically in the KLRG1hi effector CD8+ T
cell subset. more…
Organism: Mus musculus
Type: Expression profiling by array
Platform: GPL6246
Accession: GSE72162
ID: 200072162
To better elucidate epigenetic
mechanisms that correlate with the dynamic gene expression program observed
after T cell activation, we investigated the genomic landscape of histone
modifications in antigen-experienced CD8+ T cells. Using a ChIP-Seq approach
coupled with global gene expression profiling, we generated genome-wide histone
H3 lysine 4 (H3K4me3) and H3 lysine 27 (H3K27me3) trimethylation maps in
distinct subsets of CD8+ T cells-naïve, stem cell memory, central memory, and effector
memory-to gain insight into how histone architecture is remodeled during the
differentiation of activated T cells. more…
Organism: Mus musculus
Type: Expression profiling by array
Platform: GPL6246
Accession: GSE67825
ID: 200067825
Adoptive cell immunotherapy (ACT) using
autologous tumor-infiltrating lymphocytes (TIL) can result in complete
regression of advanced melanoma in some patients, but the efficacy of this
potentially curative therapy is limited by poor persistence of TIL after
adoptive-transfer. Pharmacologic inhibition of the serine/threonine kinase Akt
has recently been shown to promote immunologic memory in viral-specific murine
models, but whether this approach may enhance features of memory (e.g. more…
Organism: Homo sapiens
Type: Expression profiling by array
Platform: GPL6244
Accession: GSE60977
ID: 200060977
Cish inhibits CD8+ T cell immunity and disrupts proximal
T cell receptor signaling
T cell receptor (TCR) signaling is a
critical process in immunity to infectious disease and cancer. Recently, a
genome-wide association study has implicated polymorphisms in the CISH locus
with susceptibility to infectious diseases. However, the role of Cish in the
immune responses and its molecular underpinnings remains unclear. Here we
demonstrate that Cish deletion resulted in protection against viral infection
and enhanced CD8+ T cell tumor immunity. more…
Organism: Mus musculus
Type: Expression profiling by array
Platform: GPL6246
Accession: GSE56328
ID: 200056328
The kinase DYRK1A reciprocally regulates the
differentiation of Th17 and regulatory T cells [seq]
Using an unbiased chemical biology
approach, we discover harmine as a novel regulator of Treg/Th17
differentiation. Harmine enhances Treg differentiation (working in conjunction
with low levels of exogenous TGFb) and inhibits Th17 differentiation. Analysis
of global gene expression of Tregs generated using low TGFb + harmine reveals
significant similarity to Tregs generated using high TGFb only and suggests
relevance of harmine-engaged mechanisms to IBD.
Organism: Mus musculus
Type: Expression profiling by high
throughput sequencing
Platform: GPL16417
Accession: GSE67960
ID: 200067960
The kinase DYRK1A reciprocally regulates the
differentiation of Th17 and regulatory T cells [array]
Using an unbiased chemical biology
approach, we discover harmine as a novel regulator of Treg/Th17
differentiation. Harmine enhances Treg differentiation (working in conjunction
with low levels of exogenous TGFb) and inhibits Th17 differentiation. Analysis
of global gene expression of Tregs generated using low TGFb + harmine reveals
significant similarity to Tregs generated using high TGFb only and suggests
relevance of harmine-engaged mechanisms to IBD.
Organism: Mus musculus
Type: Expression profiling by array
Platform: GPL6887
Accession: GSE64247
ID: 200064247
We investigated the genomic landscape
of histone modifications in antigen-experienced CD8+ T cells. Using a ChIP-Seq
approach coupled with global gene expression profiling [GSE67825], we generated
genome-wide histone H3 lysine 4 (H3K4me3) and H3 lysine 27 (H3K27me3)
trimethylation maps in distinct subsets of CD8+ T cells - naïve, stem cell
memory, central memory, and effector memory.
Organism: Mus musculus
Type: Genome binding/occupancy
profiling by high throughput sequencing
Platform: GPL9185
Accession: GSE67881
ID: 200067881
Type-1-cytokines synergize with oncogene inhibition to
induce tumor growth arrest
Both targeted inhibition of oncogenic
driver mutations and immune-based therapies show efficacy in treatment of
patients with metastatic cancer but responses are either short-lived or
incompletely effective. Oncogene inhibition can augment the efficacy of
immune-based therapy but mechanisms by which these two interventions might
cooperate are incompletely resolved. Using a novel transplantable BRAFV600E-mutant
murine melanoma model (SB-3123), we explore potential mechanisms of synergy
between the selective BRAFV600E inhibitor vemurafenib and adoptive cell
transfer (ACT)-based immunotherapy. more…
Organism: Mus musculus
Type: Expression profiling by array
Platform: GPL6246
Accession: GSE62249
ID: 200062249
Stretch-Enhancers Delineate Disease-Associated Regulatory
Nodes in T Cells
T Cell stretch-enhancers are vulnerable
to Jak inhibitor tofacitinib
Organism: Homo sapiens; Mus musculus
Type: Expression profiling by high
throughput sequencing; Genome binding/occupancy profiling by high throughput
sequencing
Platforms: GPL9250 GPL13112 GPL11154
Accession: GSE60482
ID: 200060482
The role of FoxP3+ regulatory T (Treg)
cells in the maintenance of immunological tolerance is well established.
Recently, genome-wide association studies (GWAS) in humans have associated
polymorphisms within the BACH2 locus encoding the transcription factor BTB and
CNC homology 1, basic leucine zipper transcription factor 2 (Bach2) with
diverse allergic and autoimmune diseases including asthma, multiple sclerosis,
Crohn’s disease, celiac disease, generalized vitiligo and type 1 diabetes. more…
Organism: Mus musculus
Type: Expression profiling by array
Platform: GPL6246
Accession: GSE42598
ID: 200042598
Retinoic acid determines the in vivo fate-commitment of
splenic pre-dendritic cells
Comparison of gene expression changes
of FACS sorted splenic CD11b+CD8a- and CD11b-CD8a+ cDC subsets reconstituted in
vivo following total body irradiation in combination with exogenous retinoic
acid or vehicle control.
Organism: Mus musculus
Type: Expression profiling by array
Platform: GPL6246
Accession: GSE41021
ID: 200041021
CD8+ T-cell memory bears the transcriptional imprint of
progressive differentiation
The generation of CD8+ T-cell memory is
an important aim of immunization. While several distinct subsets of CD8+ T-cell
memory have been described, the lineage relationships between effector (EFF),
effector memory (EM) and central memory (CM) T cells remain contentious.
Specifically, there is contradictory experimental evidence to support both the
linear (Naive>EFF>EM>CM) and progressive differentiation
(Naive>CM>EM>EFF) models. more…
Organism: Mus musculus
Type: Expression profiling by array
Platform: GPL8389
Accession: GSE42459
ID: 200042459
Bach2 represses effector programmes to stabilize
Treg-mediated immune homeostasis
Through their functional
diversification, CD4+ T cells play key roles in both driving and constraining
immune-mediated pathology. Transcription factors are critical in the generation
and maintenance of cellular diversity and negative regulators antagonistic to
alternate fates often act in conjunction with positive regulators to stabilize
lineage specification1. Polymorphisms within the locus encoding a transcription
factor BACH2 are associated with diverse immune-mediated diseases including
asthma2, multiple sclerosis3, Crohn¹s disease4-5, coeliac disease6, vitiligo7
and type 1 diabetes8. more…
Organism: Mus musculus
Type: Expression profiling by high
throughput sequencing; Genome binding/occupancy profiling by high throughput
sequencing
Platform: GPL13112
Accession: GSE45975
ID: 200045975
Permissivity of the NCI-60 cancer cell lines to oncolytic
Vaccinia Virus GLV-1h68
Oncolytic viral therapy represents an
alternative therapeutic strategy for the treatment of cancer. This therapy
relies on efficient replication of virus in tumor cells in vivo with minimal or
no replication in normal tissues. We recently described GLV-1h68 as a modified
Vaccinia Virus (VACV) construct with exclusive in vivo tropism for tumor cells
in experimental animal models. Moreover, we had previously observed a cell
line-specific relationship between the ability of GLV-1h68 to replicate in
vitro during the first 20 hours following infection and the in vivo ability to
colonize and eliminate the corresponding tumor implant. more…
Organism: Homo sapiens
Type: Expression profiling by array
Platform: GPL13224
Accession: GSE28472
ID:200028472
Expression data from in vitro and ex vivo Th1- and
Th17-polarized TRP1 TCR transgenic CD4+ cells
Serial comparison between Th1 and Th17
tumor-specific cells cultured in vitro and ex vivo after transferred into
sublethaly irradiated B6.PL mice. Th17-derived cells acquire Th1-like
properties in vivo but maintain a distinct molecular profile.
Organism: Mus musculus
Type: Expression profiling by array
Platform: GPL6246
Accession: GSE26030
ID: 200026030
© 2016 Roychoudhuri Lab. Site hosted on Github and run on Jekyll. About the website.