| 3' -UTR-mediated translational regulation |
Pathways_-_Reactome.gmt.txt |
-3.5 |
0.00951 |
68.0 |
20.0 |
9.66 |
| Activation of Chaperone Genes by XBP1(S) |
Pathways_-_Reactome.gmt.txt |
-2.5 |
0.03235 |
32.0 |
10.0 |
4.55 |
| Activation of Chaperones by IRE1alpha |
Pathways_-_Reactome.gmt.txt |
-2.5 |
0.03235 |
32.0 |
10.0 |
4.55 |
| Association of TriC/CCT with target proteins during biosynthesis |
Pathways_-_Reactome.gmt.txt |
-2.5 |
0.02903 |
19.0 |
7.0 |
2.7 |
| BIOCARTA EIF2 PATHWAY |
Pathways_-_KEGGBioCarta.gmt.txt |
-2.7 |
0.03521 |
8.0 |
4.0 |
1.14 |
| BIOCARTA FCER1 PATHWAY |
Pathways_-_KEGGBioCarta.gmt.txt |
-2.5 |
0.0406 |
19.0 |
7.0 |
2.7 |
| BIOCARTA FMLP PATHWAY |
Pathways_-_KEGGBioCarta.gmt.txt |
-2.4 |
0.0481 |
20.0 |
7.0 |
2.84 |
| BIOCARTA GCR PATHWAY |
Pathways_-_KEGGBioCarta.gmt.txt |
-3.7 |
0.01538 |
11.0 |
6.0 |
1.56 |
| BIOCARTA RNA PATHWAY |
Pathways_-_KEGGBioCarta.gmt.txt |
-3.0 |
0.02854 |
7.0 |
4.0 |
0.99 |
| BIOCARTA TCR PATHWAY |
Pathways_-_KEGGBioCarta.gmt.txt |
-2.6 |
0.0404 |
27.0 |
9.0 |
3.83 |
| BIOPOLYMER METABOLIC PROCESS |
GO_-_Biological_Process.gmt.txt |
-4.7 |
0.00617 |
813.0 |
155.0 |
115.47 |
| CELLULAR MACROMOLECULE METABOLIC PROCESS |
GO_-_Biological_Process.gmt.txt |
-3.1 |
0.0415 |
530.0 |
100.0 |
75.28 |
| CELLULAR PROTEIN METABOLIC PROCESS |
GO_-_Biological_Process.gmt.txt |
-3.0 |
0.04249 |
525.0 |
99.0 |
74.57 |
| CELLULAR RESPONSE TO NUTRIENT LEVELS |
GO_-_Biological_Process.gmt.txt |
-1.7976931348623157E308 |
0.0 |
3.0 |
3.0 |
0.43 |
| CELL CYCLE ARREST GO 0007050 |
GO_-_Biological_Process.gmt.txt |
-3.2 |
0.03935 |
31.0 |
11.0 |
4.4 |
| CELL CYCLE GO 0007049 |
GO_-_Biological_Process.gmt.txt |
-3.5 |
0.02938 |
169.0 |
40.0 |
24.0 |
| CONDENSED NUCLEAR CHROMOSOME |
GO_-_Cellular_Component.gmt.txt |
-4.0 |
0.00461 |
10.0 |
6.0 |
1.42 |
| CYTOPLASMIC PART |
GO_-_Cellular_Component.gmt.txt |
-2.6 |
0.03799 |
709.0 |
126.0 |
100.7 |
| Calnexin/calreticulin cycle |
Pathways_-_Reactome.gmt.txt |
-2.7 |
0.02439 |
8.0 |
4.0 |
1.14 |
| Cap-dependent Translation Initiation |
Pathways_-_Reactome.gmt.txt |
-3.3 |
0.01118 |
75.0 |
21.0 |
10.65 |
| Cleavage of the damaged purine |
Pathways_-_Reactome.gmt.txt |
-1.7976931348623157E308 |
0.0 |
3.0 |
3.0 |
0.43 |
| DAMAGED DNA BINDING |
GO_-_Molecular_Function.gmt.txt |
-2.7 |
0.04505 |
11.0 |
5.0 |
1.56 |
| Depurination |
Pathways_-_Reactome.gmt.txt |
-1.7976931348623157E308 |
0.0 |
3.0 |
3.0 |
0.43 |
| Displacement of DNA glycosylase by APE1 |
Pathways_-_Reactome.gmt.txt |
-2.3 |
0.03737 |
6.0 |
3.0 |
0.85 |
| Eukaryotic Translation Elongation |
Pathways_-_Reactome.gmt.txt |
-3.4 |
0.00987 |
55.0 |
17.0 |
7.81 |
| Eukaryotic Translation Initiation |
Pathways_-_Reactome.gmt.txt |
-3.3 |
0.01118 |
75.0 |
21.0 |
10.65 |
| Eukaryotic Translation Termination |
Pathways_-_Reactome.gmt.txt |
-3.1 |
0.01298 |
53.0 |
16.0 |
7.53 |
| Formation of a pool of free 40S subunits |
Pathways_-_Reactome.gmt.txt |
-2.8 |
0.01955 |
61.0 |
17.0 |
8.66 |
| GGGCGGR V$SP1 Q6 |
TFmiRNA_Targets.gmt.txt |
-6.3 |
0.00326 |
1055.0 |
203.0 |
149.85 |
| GTP hydrolysis and joining of the 60S ribosomal subunit |
Pathways_-_Reactome.gmt.txt |
-3.4 |
0.01001 |
69.0 |
20.0 |
9.8 |
| Gene Expression |
Pathways_-_Reactome.gmt.txt |
-4.2 |
0.00492 |
484.0 |
98.0 |
68.74 |
| HIV human PPI All |
HIV_Collection.gmt.txt |
-2.6 |
0.0337 |
290.0 |
58.0 |
41.19 |
| HYDROLASE ACTIVITY HYDROLYZING N GLYCOSYL COMPOUNDS |
GO_-_Molecular_Function.gmt.txt |
-2.7 |
0.04505 |
5.0 |
3.0 |
0.71 |
| Host Interactions with Influenza Factors |
Pathways_-_Reactome.gmt.txt |
-2.7 |
0.02169 |
5.0 |
3.0 |
0.71 |
| INTRACELLULAR ORGANELLE PART |
GO_-_Cellular_Component.gmt.txt |
-4.0 |
0.00489 |
665.0 |
127.0 |
94.45 |
| IRS-mediated signalling |
Pathways_-_Reactome.gmt.txt |
-2.4 |
0.03389 |
37.0 |
11.0 |
5.26 |
| IRS-related events |
Pathways_-_Reactome.gmt.txt |
-2.4 |
0.03389 |
37.0 |
11.0 |
5.26 |
| Influenza Infection |
Pathways_-_Reactome.gmt.txt |
-3.0 |
0.01417 |
93.0 |
24.0 |
13.21 |
| Influenza Life Cycle |
Pathways_-_Reactome.gmt.txt |
-2.3 |
0.03787 |
88.0 |
21.0 |
12.5 |
| Influenza Viral RNA Transcription and Replication |
Pathways_-_Reactome.gmt.txt |
-2.8 |
0.01955 |
61.0 |
17.0 |
8.66 |
| Insulin receptor signalling cascade |
Pathways_-_Reactome.gmt.txt |
-2.6 |
0.02733 |
40.0 |
12.0 |
5.68 |
| KEGG GLIOMA |
Pathways_-_KEGGBioCarta.gmt.txt |
-3.8 |
0.01271 |
31.0 |
12.0 |
4.4 |
| KEGG MELANOMA |
Pathways_-_KEGGBioCarta.gmt.txt |
-2.7 |
0.0349 |
26.0 |
9.0 |
3.69 |
| KEGG MTOR SIGNALING PATHWAY |
Pathways_-_KEGGBioCarta.gmt.txt |
-2.4 |
0.04813 |
33.0 |
10.0 |
4.69 |
| KEGG NICOTINATE AND NICOTINAMIDE METABOLISM |
Pathways_-_KEGGBioCarta.gmt.txt |
-2.7 |
0.03521 |
8.0 |
4.0 |
1.14 |
| KEGG NON SMALL CELL LUNG CANCER |
Pathways_-_KEGGBioCarta.gmt.txt |
-3.2 |
0.02462 |
27.0 |
10.0 |
3.83 |
| KEGG N GLYCAN BIOSYNTHESIS |
Pathways_-_KEGGBioCarta.gmt.txt |
-3.0 |
0.02854 |
28.0 |
10.0 |
3.98 |
| KEGG RIBOSOME |
Pathways_-_KEGGBioCarta.gmt.txt |
-2.7 |
0.035 |
53.0 |
15.0 |
7.53 |
| L13a-mediated translational silencing of Ceruloplasmin expression |
Pathways_-_Reactome.gmt.txt |
-3.5 |
0.00951 |
68.0 |
20.0 |
9.66 |
| MACROMOLECULAR COMPLEX |
GO_-_Cellular_Component.gmt.txt |
-5.9 |
1.8E-4 |
493.0 |
107.0 |
70.02 |
| MEMBRANE ENCLOSED LUMEN |
GO_-_Cellular_Component.gmt.txt |
-4.0 |
0.00461 |
274.0 |
61.0 |
38.92 |
| MITOCHONDRIAL LUMEN |
GO_-_Cellular_Component.gmt.txt |
-4.2 |
0.0039 |
29.0 |
12.0 |
4.12 |
| MITOCHONDRIAL MATRIX |
GO_-_Cellular_Component.gmt.txt |
-4.2 |
0.0039 |
29.0 |
12.0 |
4.12 |
| MITOCHONDRIAL PART |
GO_-_Cellular_Component.gmt.txt |
-3.1 |
0.01889 |
87.0 |
23.0 |
12.36 |
| MITOCHONDRIAL RIBOSOME |
GO_-_Cellular_Component.gmt.txt |
-3.7 |
0.00679 |
17.0 |
8.0 |
2.41 |
| MITOCHONDRIAL SMALL RIBOSOMAL SUBUNIT |
GO_-_Cellular_Component.gmt.txt |
-2.7 |
0.03723 |
8.0 |
4.0 |
1.14 |
| MITOCHONDRION |
GO_-_Cellular_Component.gmt.txt |
-3.2 |
0.01679 |
208.0 |
46.0 |
29.54 |
| MITOTIC CELL CYCLE |
GO_-_Biological_Process.gmt.txt |
-3.0 |
0.04249 |
88.0 |
23.0 |
12.5 |
| Metabolism of RNA |
Pathways_-_Reactome.gmt.txt |
-2.2 |
0.04176 |
178.0 |
37.0 |
25.28 |
| Metabolism of nucleotides |
Pathways_-_Reactome.gmt.txt |
-2.4 |
0.03389 |
37.0 |
11.0 |
5.26 |
| Metabolism of proteins |
Pathways_-_Reactome.gmt.txt |
-4.5 |
0.00318 |
248.0 |
58.0 |
35.22 |
| Mitotic Telophase /Cytokinesis |
Pathways_-_Reactome.gmt.txt |
-1.7976931348623157E308 |
0.0 |
3.0 |
3.0 |
0.43 |
| NEGATIVE REGULATION OF CELL CYCLE |
GO_-_Biological_Process.gmt.txt |
-3.7 |
0.02707 |
40.0 |
14.0 |
5.68 |
| NUCLEAR LUMEN |
GO_-_Cellular_Component.gmt.txt |
-2.4 |
0.04861 |
231.0 |
47.0 |
32.81 |
| NUCLEAR PART |
GO_-_Cellular_Component.gmt.txt |
-3.8 |
0.00581 |
335.0 |
71.0 |
47.58 |
| NUCLEOBASENUCLEOSIDENUCLEOTIDE AND NUCLEIC ACID METABOLIC PROCESS |
GO_-_Biological_Process.gmt.txt |
-5.7 |
0.00119 |
620.0 |
128.0 |
88.06 |
| NUCLEUS |
GO_-_Cellular_Component.gmt.txt |
-7.8 |
1.0E-5 |
751.0 |
159.0 |
106.67 |
| Nicotinate metabolism |
Pathways_-_Reactome.gmt.txt |
-1.7976931348623157E308 |
0.0 |
3.0 |
3.0 |
0.43 |
| Nonsense Mediated Decay Independent of the Exon Junction Complex |
Pathways_-_Reactome.gmt.txt |
-2.7 |
0.02434 |
58.0 |
16.0 |
8.24 |
| ORGANELLAR RIBOSOME |
GO_-_Cellular_Component.gmt.txt |
-3.7 |
0.00679 |
17.0 |
8.0 |
2.41 |
| ORGANELLAR SMALL RIBOSOMAL SUBUNIT |
GO_-_Cellular_Component.gmt.txt |
-2.7 |
0.03723 |
8.0 |
4.0 |
1.14 |
| ORGANELLE LUMEN |
GO_-_Cellular_Component.gmt.txt |
-4.0 |
0.00461 |
274.0 |
61.0 |
38.92 |
| ORGANELLE PART |
GO_-_Cellular_Component.gmt.txt |
-4.0 |
0.00489 |
665.0 |
127.0 |
94.45 |
| PEPTIDYL AMINO ACID MODIFICATION |
GO_-_Biological_Process.gmt.txt |
-3.7 |
0.02707 |
28.0 |
11.0 |
3.98 |
| PHOSPHOTRANSFERASE ACTIVITY PHOSPHATE GROUP AS ACCEPTOR |
GO_-_Molecular_Function.gmt.txt |
-2.7 |
0.0476 |
8.0 |
4.0 |
1.14 |
| PI3K Cascade |
Pathways_-_Reactome.gmt.txt |
-2.9 |
0.01886 |
29.0 |
10.0 |
4.12 |
| PKB-mediated events |
Pathways_-_Reactome.gmt.txt |
-2.7 |
0.02203 |
18.0 |
7.0 |
2.56 |
| PROTEIN COMPLEX |
GO_-_Cellular_Component.gmt.txt |
-4.3 |
0.00364 |
423.0 |
88.0 |
60.08 |
| PROTEIN METABOLIC PROCESS |
GO_-_Biological_Process.gmt.txt |
-3.1 |
0.0415 |
573.0 |
107.0 |
81.39 |
| Peptide chain elongation |
Pathways_-_Reactome.gmt.txt |
-3.1 |
0.01298 |
53.0 |
16.0 |
7.53 |
| Post-Elongation Processing of Intronless pre-mRNA |
Pathways_-_Reactome.gmt.txt |
-2.2 |
0.04176 |
13.0 |
5.0 |
1.85 |
| Processing of Capped Intronless Pre-mRNA |
Pathways_-_Reactome.gmt.txt |
-2.2 |
0.04176 |
13.0 |
5.0 |
1.85 |
| Processing of Intronless Pre-mRNAs |
Pathways_-_Reactome.gmt.txt |
-2.4 |
0.03515 |
9.0 |
4.0 |
1.28 |
| Protein folding |
Pathways_-_Reactome.gmt.txt |
-2.7 |
0.02203 |
30.0 |
10.0 |
4.26 |
| RCGCANGCGY V$NRF1 Q6 |
TFmiRNA_Targets.gmt.txt |
-3.6 |
0.04593 |
342.0 |
71.0 |
48.58 |
| RIBONUCLEOPROTEIN COMPLEX |
GO_-_Cellular_Component.gmt.txt |
-4.6 |
0.00173 |
80.0 |
25.0 |
11.36 |
| RIBOSOMAL SUBUNIT |
GO_-_Cellular_Component.gmt.txt |
-3.4 |
0.01174 |
15.0 |
7.0 |
2.13 |
| RIBOSOME |
GO_-_Cellular_Component.gmt.txt |
-3.9 |
0.00581 |
27.0 |
11.0 |
3.83 |
| RNA BINDING |
GO_-_Molecular_Function.gmt.txt |
-2.7 |
0.04505 |
135.0 |
31.0 |
19.17 |
| RNA BIOSYNTHETIC PROCESS |
GO_-_Biological_Process.gmt.txt |
-3.0 |
0.04249 |
309.0 |
63.0 |
43.89 |
| RNA METABOLIC PROCESS |
GO_-_Biological_Process.gmt.txt |
-3.1 |
0.0415 |
414.0 |
81.0 |
58.8 |
| Recognition and association of DNA glycosylase with site containing an affected purine |
Pathways_-_Reactome.gmt.txt |
-1.7976931348623157E308 |
0.0 |
3.0 |
3.0 |
0.43 |
| Recycling of eIF2:GDP |
Pathways_-_Reactome.gmt.txt |
-2.3 |
0.03737 |
6.0 |
3.0 |
0.85 |
| Removal of DNA patch containing abasic residue |
Pathways_-_Reactome.gmt.txt |
-2.2 |
0.04176 |
13.0 |
5.0 |
1.85 |
| Resolution of AP sites via the multiple-nucleotide patch replacement pathway |
Pathways_-_Reactome.gmt.txt |
-2.2 |
0.04176 |
13.0 |
5.0 |
1.85 |
| Ribosomal scanning and start codon recognition |
Pathways_-_Reactome.gmt.txt |
-3.2 |
0.01135 |
39.0 |
13.0 |
5.54 |
| S6K1-mediated signalling |
Pathways_-_Reactome.gmt.txt |
-3.5 |
0.00951 |
6.0 |
4.0 |
0.85 |
| SIGNAL SEQUENCE BINDING |
GO_-_Molecular_Function.gmt.txt |
-3.0 |
0.03452 |
10.0 |
5.0 |
1.42 |
| SMALL NUCLEAR RIBONUCLEOPROTEIN COMPLEX |
GO_-_Cellular_Component.gmt.txt |
-3.0 |
0.02064 |
13.0 |
6.0 |
1.85 |
| SMALL RIBOSOMAL SUBUNIT |
GO_-_Cellular_Component.gmt.txt |
-2.7 |
0.03723 |
8.0 |
4.0 |
1.14 |
| SRP-dependent cotranslational protein targeting to membrane |
Pathways_-_Reactome.gmt.txt |
-2.7 |
0.02203 |
67.0 |
18.0 |
9.52 |
| STRUCTURAL CONSTITUENT OF RIBOSOME |
GO_-_Molecular_Function.gmt.txt |
-4.5 |
0.0108 |
55.0 |
19.0 |
7.81 |
| STRUCTURAL MOLECULE ACTIVITY |
GO_-_Molecular_Function.gmt.txt |
-3.3 |
0.03238 |
94.0 |
25.0 |
13.35 |
| S PHASE |
GO_-_Biological_Process.gmt.txt |
-3.8 |
0.02583 |
8.0 |
5.0 |
1.14 |
| S PHASE OF MITOTIC CELL CYCLE |
GO_-_Biological_Process.gmt.txt |
-4.3 |
0.01315 |
7.0 |
5.0 |
0.99 |
| Signaling by Insulin receptor |
Pathways_-_Reactome.gmt.txt |
-3.0 |
0.01417 |
54.0 |
16.0 |
7.67 |
| Synthesis and interconversion of nucleotide di- and triphosphates |
Pathways_-_Reactome.gmt.txt |
-2.2 |
0.04176 |
13.0 |
5.0 |
1.85 |
| TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling |
Pathways_-_Reactome.gmt.txt |
-2.3 |
0.03737 |
6.0 |
3.0 |
0.85 |
| TRANSCRIPTION |
GO_-_Biological_Process.gmt.txt |
-4.1 |
0.01565 |
363.0 |
77.0 |
51.56 |
| TRANSCRIPTION DNA DEPENDENT |
GO_-_Biological_Process.gmt.txt |
-3.1 |
0.0415 |
307.0 |
63.0 |
43.6 |
| TRANSCRIPTION INITIATION FROM RNA POLYMERASE II PROMOTER |
GO_-_Biological_Process.gmt.txt |
-3.4 |
0.03274 |
15.0 |
7.0 |
2.13 |
| TRANSLATION |
GO_-_Biological_Process.gmt.txt |
-3.3 |
0.03473 |
99.0 |
26.0 |
14.06 |
| TRANSLATION INITIATION FACTOR ACTIVITY |
GO_-_Molecular_Function.gmt.txt |
-2.7 |
0.04505 |
18.0 |
7.0 |
2.56 |
| Transcription |
Pathways_-_Reactome.gmt.txt |
-2.3 |
0.03945 |
99.0 |
23.0 |
14.06 |
| Translation |
Pathways_-_Reactome.gmt.txt |
-3.9 |
0.00596 |
97.0 |
27.0 |
13.78 |
| Translation initiation complex formation |
Pathways_-_Reactome.gmt.txt |
-3.2 |
0.01135 |
39.0 |
13.0 |
5.54 |
| Unfolded Protein Response |
Pathways_-_Reactome.gmt.txt |
-2.9 |
0.01877 |
51.0 |
15.0 |
7.24 |
| V$E2F 03 |
TFmiRNA_Targets.gmt.txt |
-3.4 |
0.04965 |
88.0 |
24.0 |
12.5 |
| V$E2F Q6 01 |
TFmiRNA_Targets.gmt.txt |
-3.7 |
0.03979 |
85.0 |
24.0 |
12.07 |
| V$NRF2 01 |
TFmiRNA_Targets.gmt.txt |
-4.3 |
0.01708 |
97.0 |
28.0 |
13.78 |
| V$TEL2 Q6 |
TFmiRNA_Targets.gmt.txt |
-3.5 |
0.0479 |
87.0 |
24.0 |
12.36 |
| Viral mRNA Translation |
Pathways_-_Reactome.gmt.txt |
-3.3 |
0.01135 |
52.0 |
16.0 |
7.39 |
| chr11q13 |
Chromosomal_Bands.gmt.txt |
-2.3 |
0.03202 |
94.0 |
22.0 |
13.35 |
| chr15q24 |
Chromosomal_Bands.gmt.txt |
-2.0 |
0.0492 |
23.0 |
7.0 |
3.27 |
| chr19p13 |
Chromosomal_Bands.gmt.txt |
-2.4 |
0.028 |
191.0 |
40.0 |
27.13 |
| chr19q13 |
Chromosomal_Bands.gmt.txt |
-6.8 |
4.0E-5 |
208.0 |
57.0 |
29.54 |
| chr1p34 |
Chromosomal_Bands.gmt.txt |
-2.8 |
0.01797 |
56.0 |
16.0 |
7.95 |
| chr3p23 |
Chromosomal_Bands.gmt.txt |
-2.0 |
0.04574 |
7.0 |
3.0 |
0.99 |
| chr6p21 |
Chromosomal_Bands.gmt.txt |
-3.5 |
0.0089 |
133.0 |
33.0 |
18.89 |
| chr9q34 |
Chromosomal_Bands.gmt.txt |
-2.4 |
0.028 |
86.0 |
21.0 |
12.21 |
| hsa-let-7b-5p targets |
TarBase_6beta.gmt.txt |
-3.6 |
0.01523 |
245.0 |
54.0 |
34.8 |
| hsa-miR-124-3p targets |
TarBase_6beta.gmt.txt |
-3.4 |
0.01713 |
548.0 |
105.0 |
77.84 |
| hsa-miR-7-5p targets |
TarBase_6beta.gmt.txt |
-3.1 |
0.03285 |
177.0 |
40.0 |
25.14 |
| mRNA Decay by 3' to 5' Exoribonuclease |
Pathways_-_Reactome.gmt.txt |
-3.0 |
0.01417 |
7.0 |
4.0 |
0.99 |
| mTOR signalling |
Pathways_-_Reactome.gmt.txt |
-2.7 |
0.02203 |
18.0 |
7.0 |
2.56 |
| mTORC1-mediated signalling |
Pathways_-_Reactome.gmt.txt |
-3.0 |
0.01417 |
7.0 |
4.0 |
0.99 |
Figure: Temporal expression patterns were grouped into clusters with differential expression profiles at
three phases of the viral life cycle, namely reverse transcription, integration, and late phase.
Boxplots on the left show the distribution of the normalized regression weights for each viral phase used in clustering.
Expression change pattern of each gene over time is plotted for mock and HIV samples (dotted orange lines) along with the cluster median (bold red line).