Case study

The MIT/ICBP siRNA Database is an database of experimentally tested siRNAs containing information about genes, siRNA sequence, mRNA and Protein knockdown efficay. Currently the database has validated siRNA and shRNA sequences against over 100 genes from three sources.

We have selected 90 siRNAs that are experimentally designed as test case to demonstrate the utlity of siRNA design module in FusionHub. These siRNAs target 63 genes.

Each of these genes were submitted to siRNA design module of FusionHub using all the 4 siRNA prediction tool with default parameter settings.

Of the 90 siRNAs,


The table below shows the results.
Column1: Gene
Column2: Link to MIT/ICBP siRNA Database
Column3: Target sequence for siRNA
Column4: mRNA knock down efficiency
Column5: protein knock down efficiency
Column6: Target sequence location for siRNA
Column7: List of tools which correctly predicted the siRNA
Column8: Total count of tools
Column9: Link to results of FusionHub siRNA designing module
Column10: Gene Sequence

Target_GenesiRNA_IDTarget_seq_for_sirnamRNA
knockdown
Protein
knockdown
Target
pos
Predicted byTool
count
Prediction
Result
Target
Sequence
ARHGDIB 1026 CAGCTGGGTCCCTCTTCAA90-100%---794Biltr, Rnaxs2 Case_1026 View
CD82/KAI1 1024 CAAGGGTGTGTATATTGTA90-100%---1354Biltr, Rnaxs2 Case_1024 View
HSP90A 1025 AGAAATAGGTTAAACTGAA90-100%---2839Biltr, Rnaxs2 Case_1025 View
ITGB1 1023 GGATATTACTCAGATCCAA90-100%-----0Case_1023 View
RHOA 1027 CGGAATGATGAGCACACAA90-100%---640Biltr, Rnaxs2 Case_1027 View
XRN-1 beta 1006 GTACCTGGATATACTAAGA90-100%-----0 Case_1006 View
XRN-1 delta 1007 CUACUCAAGUACCUACUAA90-100%-----0 Case_1007 View
YWHAZ 1022 GGTTTATGTTACTTCTATT90-100%70-80%925Biltr, Rnaxs, Sidirect3 Case_1022 View
ABCB1 1053 CGAACACATTGGAAGGAAA80-90%---3501Biltr, Rnaxs2 Case_1053 View
AKT2 1047 GGATGAAGTCGCTCACACA80-90%---872Biltr, Rnaxs2 Case_1047 View
ARD1A 1049 AGATGAAATACTACTTCTA80-90%---191Biltr, Rnaxs2 Case_1049 View
ARHGDIB 1066 CTGAATAAATAGATCAGAA80-90%---87Biltr, Rnaxs2 Case_1066 View
ARHGEF12 1067 GAGAGTCACCAACAGATAA80-90%---412-0Case_1067 View
ASNS 1060 GGATACTGCCAATAAGAAA80-90%---558Biltr, Rnaxs, Sidirect3 Case_1060 View
BAD 1034 GAGTTTGTGGACTCCTTTA80-90%---599Biltr, Ernai2 Case_1034 View
BAG3 1052 GCAAAGAGGTGGATTCTAA80-90%---1334Biltr, Sidirect2 Case_1052 View
BAG3 1046 CGATGTGTGCTTTAGGGAA80-90%---2065-0Case_1046 View
BAG4 1065 GGATATAATCTGAGACAAA80-90%---2003Biltr, Rnaxs2 Case_1065 View
BAG4 1044 ACATATACTTCATGTGTAA80-90%---2086-0Case_1044 View
BRMS1 1051 GGAATAAGTACGAATGTGA80-90%---539Biltr, Rnaxs, Sidirect3 Case_1051 View
CAV1 1059 GCAACAATTTATGAATTGA80-90%---902Biltr, Rnaxs, Sidirect3 Case_1059 View
CD44v6 1002 GCAACTCCTAGTAGTACAA80-90%---1337Biltr, Rnaxs2 Case_1002 View
CD82/KAI1 1031 GGGTTCTCTTATCAACTCA80-90%---0-0Case_1031 View
CDH1 1050 GGCCTGAAGTGACTCGTAA80-90%60-70%2460-0Case_1050 View
CTNNB1 1048 CGGGATGTTCACAACCGAA80-90%70-80%2012Biltr, Rnaxs2 Case_1048 View
CTNNB1 1043 GGGTAGGGTAAATCAGTAA80-90%60-70%3557Biltr, Rnaxs2 Case_1043 View
FGFR1 1042 GAGATTTACCCATCGGGTA80-90%---3844-0Case_1042 View
FH 1063 GATCTACGATGAACTTTAA80-90%---253Biltr, Ernai, Rnaxs, Sidirect4 Case_1063 View
FH 1039 CAACGATCATGTTAATAAA80-90%---563Biltr, Ernai, Rnaxs3 Case_1039 View
GIPC1 1058 GCCGTACCTTCACGCTGAA80-90%---0-0Case_1058 View
HIF1A 1057 CGTTGTGAGTGGTATTATT80-90%---1304-0Case_1057 View
HPRT1 1045 GATTGTTGTTTAACTTGTA80-90%---961Biltr, Rnaxs, Sidirect3 Case_1045 View
HSP90A 1028 GCCCTAAGAGACAACTCAA80-90%---2042Biltr, Rnaxs2 Case_1028 View
IGF2R 1038 CGCAGGTAACGATGGGAAA80-90%---1459-0Case_1038 View
ITGB1 1056 GCGAGTGTGATAATTTCAA80-90%---1784-0Case_1056 View
KISS1 1041 GAAATGTTGCGTAACTCAA80-90%---697Biltr, Rnaxs, Sidirect3 Case_1041 View
MMP1 1055 GCGTGTGACAGTAAGCTAA80-90%---900Biltr, Rnaxs2 Case_1055 View
NME2 1037 GAGCATATTTGCCAATAAA80-90%---789Biltr, Sidirect2 Case_1037 View
NME2 1033 GCACCTTCATCGCCATCAA80-90%---241Biltr, Rnaxs2 Case_1033 View
PIK3C2A 1036 CCCACTAATTGCATTGGAA80-90%---2880-0Case_1036 View
PLK1 1030 CCATATGAATTGTACAGAA80-90%---2085Biltr, Rnaxs2 Case_1030 View
PLK1 1032 GGATCAAGAAGAATGAATA80-90%---838Biltr, Ernai, Rnaxs, Sidirect4 Case_1032 View
RB1 1035 CGTGTAAATTCTACTGCAA80-90%70-80%2027-0Case_1035 View
RB1 1040 GGGTTGTGTCGAAATTGGA80-90%70-80%1474-0Case_1040 View
RBX1 1054 GGGATATTGTGGTTGATAA80-90%---122Biltr, Ernai, Rnaxs, Sidirect4 Case_1054 View
RHA 1005 AGACGCAGAAGTTTTATGC80-90%---2574Biltr, Rnaxs2 Case_1005 View
RHOA 1029 AGCTAGACGTGGGAAGAAA80-90%---816Biltr, Rnaxs2 Case_1029 View
ABCC1 1106 GAGTGGAATTCCGGAACTA70-80%---4050Biltr, Rnaxs2 Case_1106 View
ADAM8 1085 GCATCATCGTCTACCGCAA70-80%---2107Biltr, Rnaxs2 Case_1085 View
AKT3 1097 GCAGCTCCAACTTATATAA70-80%---2612Biltr, Rnaxs2 Case_1097 View
AKT3 1098 GAGTGATCATGGAAATGTA70-80%---3313-0Case_1098 View
ANP32A 1103 GACTAAGTGGAATAACCTA70-80%---916Biltr, Sidirect2 Case_1103 View
ARHGEF12 1093 CGTTTAGCCCTGTCATTAA70-80%---3559Biltr, Sidirect2 Case_1093 View
ASNS 1082 GAAGCTAAAGGTCTTGTTA70-80%---658Biltr, Rnaxs, Sidirect3 Case_1082 View
BAG1 1092 GGGTCATGTTAATTGGGAA70-80%---728Biltr, Rnaxs2 Case_1092 View
BRMS1 1064 GGAGAAGTTGTTCAGGGAA70-80%---372-0Case_1064 View
CAV1 1069 GGAATAAGTTCAAATTCTT70-80%---2121Biltr, Sidirect2 Case_1069 View
CCND1 1079 CCTACGATACGCTACTATA70-80%---1910Biltr, Rnaxs, Sidirect3 Case_1079 View
CDK4 1078 GGTAATCCGGAGTGAGCAA70-80%---1190Biltr, Rnaxs2 Case_1078 View
CDK4 1081 GAACTGACCGGGAGATCAA70-80%---537-0Case_1081 View
CUL2 1075 GCACAATGCCCTTATTCAA70-80%---2312Biltr, Sidirect2 Case_1075 View
EGFR 1084 GGATAGTATGAGCCCTAAA70-80%70-80%3898Biltr, Rnaxs2 Case_1084 View
EGFR 1091 CCTTAGCAGTCTTATCTAA70-80%80-90%610Biltr, Rnaxs2 Case_1091 View
FMR1 1074 CGTGAATGGAGTACCCTAA70-80%---2110-0Case_1074 View
GIPC1 1090 ACATGATCGAGGCCATTAA70-80%---0-0Case_1090 View
GSK3B 1086 CACTGGTCACGTTTGGAAA70-80%70-80%2347Biltr, Rnaxs2 Case_1086 View
GSK3B 1089 GCATTTATCGTTAACCTAA70-80%80-90%895Biltr, Sidirect2 Case_1089 View
HDAC1 1102 CCCGGAGGAAAGTCTGTTA70-80%---83Biltr, Rnaxs2 Case_1102 View
IGF2R 1068 GAGTCTCGTACTATATAAA70-80%---6210Biltr, Rnaxs2 Case_1068 View
K-RAS 1105 GACGTATATTGTATCATTT70-80%---4218Biltr, Rnaxs, Sidirect3 Case_1105 View
K-RAS 1096 GAGATAACACGATGCGTAT70-80%---3460-0Case_1096 View
MAP2K1 1073 GGAAGAATTCCTGAACAAA70-80%80-90%950Biltr, Sidirect2 Case_1073 View
MAP2K1 1088 GGATCAAGTCCTGAAGAAA70-80%60-70%928Biltr, Rnaxs, Sidirect3 Case_1088 View
MAPK14 1083 CTCTCCAAATATTATTCAA70-80%---1626Biltr, Rnaxs2 Case_1083 View
MET 1072 CGAGGGAATCATCATGAAA70-80%90-100%3580-0Case_1072 View
NME1 1071 AGTTGGCAGGAACATTATA70-80%---441Biltr, Rnaxs2 Case_1071 View
P53 1099 GAGTGCATTGTGAGGGTTA70-80%80-90%1804-0Case_1099 View
RHOC 1101 CTACTGTCTTTGAGAACTA70-80%---509Biltr, Rnaxs2 Case_1101 View
SFN 1087 CATGTTTCCTCTCAATAAA70-80%---1280Biltr, Ernai, Rnaxs, Sidirect4 Case_1087 View
SFN 1100 GGGAGAAGGTGGAGACTGA70-80%---325Biltr, Rnaxs2 Case_1100 View
SMAD2 1070 ACTAGAATGTGCACCATAA70-80%---1625-0Case_1070 View
SOS1 1062 GGTTGAATCCATCACTAAA70-80%---2228Biltr, Sidirect2 Case_1062 View
SRC 1104 GCTTGTGGGTGATGTTTGA70-80%---3029Biltr, Rnaxs2 Case_1104 View
STAT1 1077 CAACTATATTATCATGCAA70-80%---3937-0Case_1077 View
STAT1 1095 GCTTGACGTAGGAACGGTA70-80%---3040Biltr, Rnaxs2 Case_1095 View
STAT3 1076 CGTCATTAGCAGAATCTCA70-80%---1021Biltr, Rnaxs2 Case_1076 View
TOP1 1080 GGAAGGACTCCATCAGATA70-80%---1842-0Case_1080 View
TOP1 1094 GGATGATGCTGATTATAAA70-80%---676Biltr, Ernai, Rnaxs3 Case_1094 View
VIL2 1061 GGACTGATTGAATTACGGA70-80%---2232Biltr, Rnaxs2 Case_1061 View
CXCR4 1000 GTTTTCACTCCAGCTAACA---90-100%0-0Case_1000 View