1. Summary
This report includes quality check for raw sequencing data (section 2), reads mapping and assignment (section 3), and expression similarity between samples (section 4). The results of differential expression analysis are summarized in section 5 using the criteria of fold change >= 2 and FDR <= 0.05 .The top five enriched elements of each category are reported in section 6.
2. Sequencing Quality
2.1 Summary of sequencing quality
3. Mapping quality
3.1 Summary of mapping quality
Table 1: The summary of RNAseq mapping results
ER1 |
42442664 |
36824968 |
5081203 |
139080 |
0.9873596 |
ER2 |
36380540 |
31647246 |
4273071 |
120329 |
0.9873497 |
ctrl1 |
35405319 |
30682282 |
4273717 |
119971 |
0.9873093 |
ctrl2 |
32544619 |
28122469 |
3946112 |
110549 |
0.9853728 |
**Ratio* |
* = (Uniquely |
mapped + Mapped to multi |
ple loci)/ Input reads |
|
|
4. Expression Quantification
4.1 Summary of reads assignment
Table 2: The summary of reads assignment to genes
ER1 |
30892781 |
93.82684 |
2032531 |
0 |
32925312 |
ER2 |
26333753 |
93.93351 |
1700709 |
0 |
28034462 |
ctrl1 |
25692584 |
93.87052 |
1677654 |
0 |
27370238 |
ctrl2 |
23361159 |
93.94516 |
1505644 |
0 |
24866803 |
4.2 Expression density of samples
4.3 Similarity between samples
5. Differential expression
5.2 Summary of differential analysis
Table 3: DEG numbers under FC > 2 & FDR < 0.05
ER_vs_ctrl_min5_fdr0.05 |
373 |
Table 4: deseq2_ER_vs_ctrl top 10 differential expressed genes
ENSG00000136997 |
MYC |
4940.9387 |
3.176374 |
0.0733927 |
43.27918 |
0 |
0 |
9.040323 |
ENSG00000182704 |
TSKU |
4811.9953 |
2.824986 |
0.0745477 |
37.89503 |
0 |
0 |
7.086073 |
ENSG00000100219 |
XBP1 |
25329.4977 |
2.069243 |
0.0574100 |
36.04328 |
0 |
0 |
4.196664 |
ENSG00000173706 |
HEG1 |
1616.6958 |
3.408640 |
0.1010199 |
33.74227 |
0 |
0 |
10.619474 |
ENSG00000113739 |
STC2 |
8169.7740 |
2.588275 |
0.0773372 |
33.46742 |
0 |
0 |
6.013791 |
ENSG00000110092 |
CCND1 |
21857.9807 |
1.767084 |
0.0553333 |
31.93525 |
0 |
0 |
3.403652 |
ENSG00000170525 |
PFKFB3 |
5455.4875 |
1.974682 |
0.0639637 |
30.87191 |
0 |
0 |
3.930417 |
ENSG00000074410 |
CA12 |
9928.4744 |
2.190397 |
0.0719953 |
30.42417 |
0 |
0 |
4.564311 |
ENSG00000164626 |
KCNK5 |
884.9953 |
4.541789 |
0.1544625 |
29.40383 |
0 |
0 |
23.292432 |
ENSG00000261578 |
RP11-21L23.2 |
865.6405 |
3.938454 |
0.1380153 |
28.53635 |
0 |
0 |
15.331784 |
6. Funcional enrichment analysis
List of the top five significantly enriched elements
6.1 WebGestalt
6.1.1 ER_vs_ctrl
Table 5: WebGestalt_GO_BP_ER_vs_ctrl
GO:0050673 |
epithelial cell proliferation |
23 |
2.96e-05 |
GO:0002521 |
leukocyte differentiation |
26 |
3.14e-05 |
GO:0050679 |
positive regulation of epithelial cell proliferation |
15 |
3.84e-05 |
GO:1902105 |
regulation of leukocyte differentiation |
18 |
3.84e-05 |
GO:0032526 |
response to retinoic acid |
12 |
6.86e-05 |
Table 7: WebGestalt_GO_MF_ER_vs_ctrl
GO:0001228 |
transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding |
19 |
0.0000578 |
GO:0001077 |
transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding |
14 |
0.0015095 |
GO:0000982 |
transcription factor activity, RNA polymerase II core promoter proximal region sequence-specific binding |
16 |
0.0043459 |
GO:0000987 |
core promoter proximal region sequence-specific DNA binding |
16 |
0.0070653 |
GO:0001159 |
core promoter proximal region DNA binding |
16 |
0.0070653 |
Table 8: WebGestalt_KEGG_ER_vs_ctrl
hsa05200 |
Pathways in cancer - Homo sapiens (human) |
20 |
0.0043714 |
hsa04923 |
Regulation of lipolysis in adipocytes - Homo sapiens (human) |
7 |
0.0069795 |
hsa05166 |
HTLV-I infection - Homo sapiens (human) |
14 |
0.0130652 |
hsa04024 |
cAMP signaling pathway - Homo sapiens (human) |
12 |
0.0130652 |
hsa04151 |
PI3K-Akt signaling pathway - Homo sapiens (human) |
15 |
0.0480313 |
6.2 GSEA
6.2.1 ER_vs_ctrl
Table 11: ER_vs_ctrl_min5_fdr0.05_DESeq2_GSEA GOGeneSets Positive-regulated
GO_PRERIBOSOME |
Any complex of pre-rRNAs, ribosomal proteins, and associated proteins formed during ribosome biogenesis. |
60 |
0.845003 |
2.361481 |
0 |
GO_RIBOSOME_BIOGENESIS |
A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits; includes transport to the sites of protein synthesis. |
298 |
0.7148912 |
2.3415384 |
0 |
GO_NUCLEOLAR_PART |
Any constituent part of a nucleolus, a small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. |
60 |
0.8183922 |
2.286099 |
0 |
GO_RRNA_METABOLIC_PROCESS |
The chemical reactions and pathways involving rRNA, ribosomal RNA, a structural constituent of ribosomes. |
248 |
0.69911313 |
2.2854564 |
0 |
GO_RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS |
A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a complex containing RNA and proteins. Includes the biosynthesis of the constituent RNA and protein molecules, and those macromolecular modifications that are involved in synthesis or assembly of the ribonucleoprotein complex. |
419 |
0.67804366 |
2.27912 |
0 |
Table 16: ER_vs_ctrl_min5_fdr0.05_DESeq2_GSEA OncogenicGeneSets Positive-regulated
MYC_UP.V1_UP |
Genes up-regulated in primary epithelial breast cancer cell culture over-expressing MYC [GeneID=4609] gene. |
150 |
0.75292045 |
2.3476157 |
0 |
IL15_UP.V1_UP |
Genes up-regulated in Sez-4 cells (T lymphocyte) that were first starved of IL2 [GeneID=3558] and then stimulated with IL15 [GeneID=3600]. |
141 |
0.69340885 |
2.1460347 |
0 |
IL2_UP.V1_UP |
Genes up-regulated in Sez-4 cells (T lymphocyte) that were first starved of IL2 [GeneID=3558] and then stimulated with IL2 [GeneID=3558]. |
131 |
0.6811118 |
2.1003718 |
0 |
LTE2_UP.V1_DN |
Genes down-regulated in MCF-7 cells (breast cancer) positive for ESR1 [GeneID=2099] MCF-7 cells (breast cancer) and long-term adapted for estrogen-independent growth. |
189 |
0.6297597 |
2.0154269 |
0 |
ERB2_UP.V1_DN |
Genes down-regulated in MCF-7 cells (breast cancer) positive for ESR1 [GeneID=2099] and engineered to express ligand-activatable ERBB2 [GeneID=2064]. |
186 |
0.6292693 |
2.0061898 |
0 |
Table 17: ER_vs_ctrl_min5_fdr0.05_DESeq2_GSEA OncogenicGeneSets Negative-regulated
MTOR_UP.N4.V1_DN |
Genes down-regulated in CEM-C1 cells (T-CLL) in comparison of control vs rapamycin (sirolimus) [PubChem=6610346], an mTOR pathway inhibitor. |
153 |
-0.53632164 |
-2.1790252 |
0 |
IL2_UP.V1_DN |
Genes down-regulated in Sez-4 cells (T lymphocyte) that were first starved of IL2 [GeneID=3558] and then stimulated with IL2 [GeneID=3558]. |
114 |
-0.5219168 |
-2.0491354 |
0 |
STK33_SKM_UP |
Genes up-regulated in SKM-1 cells (AML) after knockdown of STK33 [GeneID=65975] by RNAi. |
212 |
-0.44171953 |
-1.8461125 |
0.004439152 |
TGFB_UP.V1_DN |
Genes down-regulated in a panel of epithelial cell lines by TGFB1 [GeneID=7040]. |
153 |
-0.44098106 |
-1.8259705 |
0.003966177 |
ERB2_UP.V1_UP |
Genes up-regulated in MCF-7 cells (breast cancer) positive for ESR1 [GeneID=2099] and engineered to express ligand-activatable ERBB2 [GeneID=2064]. |
186 |
-0.43399885 |
-1.8058369 |
0.003959772 |
7. Results folder structure