1. TF-RNA

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1-1 Introduction

The "TF-RNA" module provides 51,097 ncRNAs that transcribed by 11 transcription factors (TFs) including BDP1, BRF1, BRF2, POLR3D, POLR3G, POLR3GL, RPC155, TBP, TFIIIC-110, TFIIIC-220 and TFIIIC63 in 10 cells for human, and 8,234 ncRNAs guided by 4 TFs, including POLR3D, POLR3G, POLR3GL and TBP in 4 cells for mouse.

1-2 Usage

Users can select targeted transcription factor in specific cell to gain a series of ncRNAs transcribed by this transcription factor.

Clicking the ncRNAID for detail informations about this ncRNA.

In detail page, click the location (Chrom:Start-End) to link to UCSC browser.

 

2. RNA-RBP

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2-1 Introduction

The "RNA-RBP" module presents the relationships of polIII-transcribed ncRNAs (18,055 ncRNAs of human and 3,364 ncRNAs of mouse) with RNA binding proteins (RBPs) (185 RBPs of human and 55 RBPs of mouse), which the RBPs may select and bind ncRNAs through some mechanisms for more downstream functions in human and mouse.

Detail pages provides more informations of polIII-transcribed ncRNAs, including the genomic informations, associated TFs, RBP binding sites, et,al.

2-2 Usage

Users can select targeted ncRNA type and show list of ncRNAs that are related with RBPs.

Clicking the ncRNAID for the detail informations of this interacting pair, including RBP binding sies on this ncRNA, the source of this RBP, samples, cells and conditions.

In detial page, usrs can click the "Show Detail" button to see all the TF binding sites from different datasets and cells.

In detail page, click the location (Chrom:Start-End) to link to UCSC browser.

 

3. RNA-Mod

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3-1 Introduction

The "RNA-Mod" module provides the map of RNA modifications on polIII-transcribed ncRNAs for human and mouse, which include the genomic corrdinates of RNA modification sites and its modification type, cell or tissue, source, library strategy, accuracy and other details.

NcRNAs can be decorated by variouse RNA modifications. In human, 2,310 polIII-transcribed ncRNAs are modified by 30 types of chemical groups, including 2G, ac4C, acp3U, A-I, Am, Cm, D, galQtRNA, Gm, i6A, m1A, m1G, m1I, m1Y, m2, m2G, m3C, m5C, m5U, m5Um, m6A, m7G, o2yW, QtRNA, t6A, tm5U, Um, xU, Y and Ym. While in mouse, 765 polIII-transcribed ncRNAs are decorated by 22 RNA modification types including 2G, A-I, Am, Cm, D, Gm, i6A, m1A, m1G, m2, m2G, m5C, m5U, m5Um, m6A, m7G, t6A, Um, xA, xU, Y and yW.

3-2 Usage

Users can select targeted ncRNA type and show list of ncRNAs that are decorated by diverse RNA modifications.

Clicking the ncRNAID for the detail informations of this ncRNA, as well as the genomic informations of this RNA modification site, like cell or tissue, source, library strategy, accuracy, pubmed, sequence, et.al.

In detail page, click the value of "Mod ID" (like m1A_site_932) to link to ENCORE for details about this RNA modification site.

In detail page, click the location (Chrom:Start-End) to link to UCSC browser.

 

4. tsRNA

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4-1 Introduction

The "tsRNA" module explores tRNA-derived small RNAs (tsRNAs) in different cancers. Here, it provides 11,403 tsRNAs that are produced by the degradation of 499 tRNAs from 32 tumors.

4-2 Usage

Users can select targeted polIII-transcribed tRNAs and tumors to show all tsRNAs derived from this tRNA in this tumor and their details including genomic corrdinates, sequence and types.

 

5. Expression

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5-1 Introduction

The "Expression" module offers the expression profiles of polIII-transcribed ncRNAs in 75 different cells and tissues, which are normalized by "mean" and "z-score" methods.

5-2 Usage

Users can select targeted ncRNA type and normalized method to see their expression profiles in different cells and tissues.

Clicking the ncRNAID for the detail informations of this ncRNA like genomic corrdinates and its expression plot in different cells and tissues.

In detail page, click the location (Chrom:Start-End) to link to UCSC browser.

 

6. Pan-Cancer

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6-1 Introduction

The "Pan-Cancer" module offers 2 sub-pages: ncRNA case and cancer case. "ncRNA case" provides the expression profiles of polIII-transcribed ncRNAs in 28 different tumors and their adjacent tissues, which are normalized by "mean" and "z-score" methods. While "cancer case" provides the average expression levels (log2(FPKM+1)) of all polIII-transcribed ncRNAs in this tumor and their adjacent tissues.

6-2 Usage

In "ncRNA case", users can select targeted ncRNA type and normalized method to see their expression profiles in different tumors and their adjacent tissues. Clicking the ncRNAID for the detail informations of this ncRNA like genomic corrdinates and its expression plot in different tumors and their adjacent tissues.

In "cancer case", users can select targeted tumor type to see the expression levels of all ncRNAs in this tumor and the adjacent tissues. Clicking the ncRNAID for the detail informations of this ncRNA like genomic corrdinates and its expression plot in different samples of this tumor and its adjacent tissue respectively.

 

7. Disease

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7-1 Introduction

The "Disease" module explores the 5 mutations (DEL, DNV, INS, SNV and SUBS) on 10,610 polIII-transcribed ncRNAs in 28 different diseases and cancers including ACC, ALL, AML, BRCA, CESC, CLL, CRC, DLBCL, ESCA, HCC, KICH, KIRC, LIHC, LUAD, LUSC, MED, MEL, NB, OV, PA, PET, PRAD, SARC, SCLC, SKCM, STAD, THCA and UCEC. The information of diseases came from COSMIC database.

7-2 Usage

Users can select targeted disease for all mutation sites on ncRNAs in this disease.

Clicking the ncRNAID for the detail informations of this ncRNA like genomic corrdinates and mutation occured on this it in this specific disease.

In detail page, click the location (Chrom:Start-End) to link to UCSC browser.

 

8. Evolution

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8-1 Introduction

The "Evolution" module is used to display the evolutionary conserved ncRNAs in human and mouse. Here, it provides 2,582 polIII-transcribed ncRNAs of human that are conserved with mouse polIII-transcribed ncRNAs, which include 81,738 conserved pairs. At the same time, it also provides 1,402 evolutionary conserved polIII-transcribed ncRNAs of mouse, which include 85,901 conserved pairs.

8-2 Usage

Users can select targeted ncRNA type and display all ncRNAs and their conserved pairs.

Clicking the ncRNAID for the detail informations of this ncRNA like genomic corrdinates and its conserved informations including reference ID, reference name, conserved type, score, alignment, et.al.

In detail page, click the location (Chrom:Start-End) to link to UCSC browser.

 

9. Motif

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9-1 Introduction

The "Motif" module provides the conserved concensus sequence in ncRNAs transcribed by PolIII complex.

9-2 Usage

Users can select targeted transcription factors and its correponding sample to demonstrate the ncRNAs that transcribed by this transcription factor and its consensus sequence.

Clicking on the button for the matrix files and motif logos.

 

10. Tool

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10-1 Introduction

The "Tool" module provides three search tools for users to investigate the Pol III-associated ncRNAs.

10-2 Usage

Users can input a gene ID/name (e.g., tRNA-Asn-GTT-2-3, tRNA-Asn-GTT), gene location in a UCSC compatible format (e.g., chr1:120,844,261-120,844,335 ) or gene sequence to see whether it hits annotated Pol III-associated ncRNAs in the database. The list of results will contain all Pol III-associated ncRNAs that overlap the specified gene. Users can download the list by clicking the "Download Excel" button.