Breast Invasive Carcinoma: PARADIGM pathway analysis of mRNA expression and copy number data
Maintained by TCGA GDAC Team (Broad Institute/Dana-Farber Cancer Institute/Harvard Medical School)
- Overview
+ Introduction
- Summary

There were 52 significant pathways identified in this analysis.

Table 1.  Get Full Table Top 10 out of 131 pathways in order of significance.

Pathway.Name Avg.Num.Perturbations
Signaling events regulated by Ret tyrosine kinase 95
Signaling events mediated by Stem cell factor receptor (c-Kit) 85
Endothelins 79
FOXM1 transcription factor network 75
IGF1 pathway 71
Plasma membrane estrogen receptor signaling 67
EGFR-dependent Endothelin signaling events 66
Osteopontin-mediated events 65
IL4-mediated signaling events 60
Syndecan-1-mediated signaling events 59
- Results

The following list describes the columns found in Table 2.

  • Pathway.Name = Full pathway name of curated PARADIGM pathway

  • Avg.Num.Perturbations = Average number of samples with perturbations across the pathway concepts determined by a background permutation model (>2 standard deviations away from the permuted distribution)

  • Total.Perturbations = Total number of perturbed concepts across all samples (>2 standard deviations away from the permuted distribution)

  • Num.Entities = Number of concepts that belong to the pathway

  • Min.Mean.Truth = Minimum IPL for concepts in the pathway among real samples

  • Max.Mean.Truth = Maximum IPL for concepts in the pathway among real samples

  • Min.Mean.Within = Minimum IPL for concepts in the pathway among null samples using "within permutation" (values are permuted across genes)

  • Max.Mean.Within = Maximum IPL for concepts in the pathway among null samples using "within permutation" (values are permuted across genes)

  • Min.Mean.Any = Minimum IPL for concepts in the pathway among null samples using "any permutation" (values are permuted across samples and genes)

  • Max.Mean.Any = Maximum IPL for concepts in the pathway among null samples using "any permutation" (values are permuted across samples and genes).

Table 2.  Get Full Table This summary table provides a report of cancer type specific pathway perturbations. Click on the links in the first column to display more detailed results for each pathway.

Pathway.Name Avg.Num.Perturbations Total.Perturbations Num.Entities Min.Mean.Truth Max.Mean.Truth Min.Mean.Within Max.Mean.Within Min.Mean.Any Max.Mean.Within.1
Signaling events regulated by Ret tyrosine kinase 95 7807 82 -0.16 0.036 1000 -1000 -0.041 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 85 6653 78 -0.31 0.13 1000 -1000 -0.043 -1000
Endothelins 79 7637 96 -0.18 0.035 1000 -1000 -0.029 -1000
FOXM1 transcription factor network 75 3871 51 -0.43 0.033 1000 -1000 -0.037 -1000
IGF1 pathway 71 4100 57 -0.08 0.051 1000 -1000 -0.028 -1000
Plasma membrane estrogen receptor signaling 67 5804 86 -0.22 0.21 1000 -1000 -0.034 -1000
EGFR-dependent Endothelin signaling events 66 1390 21 -0.073 0.047 1000 -1000 -0.016 -1000
Osteopontin-mediated events 65 2501 38 -0.14 0.038 1000 -1000 -0.018 -1000
IL4-mediated signaling events 60 5490 91 -0.53 0.42 1000 -1000 -0.084 -1000
Syndecan-1-mediated signaling events 59 2023 34 -0.13 0.041 1000 -1000 -0.016 -1000
HIF-1-alpha transcription factor network 56 4319 76 -0.18 0.049 1000 -1000 -0.01 -1000
Glucocorticoid receptor regulatory network 55 6277 114 -0.39 0.19 1000 -1000 -0.04 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 54 3711 68 -0.34 0.15 1000 -1000 -0.086 -1000
Signaling events mediated by the Hedgehog family 52 2715 52 -0.097 0.051 1000 -1000 -0.02 -1000
TCR signaling in naïve CD8+ T cells 49 4627 93 -0.074 0.047 1000 -1000 -0.034 -1000
Wnt signaling 49 346 7 -0.068 0.03 1000 -1000 -0.006 -1000
Thromboxane A2 receptor signaling 48 5052 105 -0.11 0.06 1000 -1000 -0.031 -1000
Fc-epsilon receptor I signaling in mast cells 47 4647 97 -0.096 0.035 1000 -1000 -0.049 -1000
Noncanonical Wnt signaling pathway 46 1201 26 -0.068 0.035 1000 -1000 -0.042 -1000
FAS signaling pathway (CD95) 46 2205 47 -0.1 0.048 1000 -1000 -0.024 -1000
IL12-mediated signaling events 45 3938 87 -0.26 0.042 1000 -1000 -0.038 -1000
Nongenotropic Androgen signaling 45 2365 52 -0.11 0.062 1000 -1000 -0.017 -1000
IL23-mediated signaling events 45 2721 60 -0.2 0.036 1000 -1000 -0.052 -1000
IL27-mediated signaling events 44 2289 51 -0.2 0.1 1000 -1000 -0.046 -1000
Stabilization and expansion of the E-cadherin adherens junction 44 3300 74 -0.095 0.058 1000 -1000 -0.05 -1000
IL6-mediated signaling events 41 3100 75 -0.14 0.037 1000 -1000 -0.033 -1000
LPA receptor mediated events 39 3991 102 -0.077 0.035 1000 -1000 -0.069 -1000
Syndecan-4-mediated signaling events 39 2640 67 -0.06 0.089 1000 -1000 -0.028 -1000
Arf6 signaling events 37 2294 62 -0.069 0.079 1000 -1000 -0.011 -1000
Signaling mediated by p38-gamma and p38-delta 37 569 15 -0.056 0.033 1000 -1000 -0.027 -1000
E-cadherin signaling in keratinocytes 37 1602 43 -0.061 0.036 1000 -1000 -0.018 -1000
Ephrin B reverse signaling 35 1699 48 -0.12 0.071 1000 -1000 -0.035 -1000
IL2 signaling events mediated by PI3K 35 2034 58 -0.23 0.035 1000 -1000 -0.031 -1000
TCGA08_p53 34 240 7 -0.029 0.026 1000 -1000 -0.003 -1000
E-cadherin signaling events 34 173 5 -0.012 0.028 1000 -1000 0.02 -1000
ErbB4 signaling events 33 2316 69 -0.11 0.06 1000 -1000 -0.02 -1000
PLK2 and PLK4 events 32 97 3 -0.015 0.03 1000 -1000 0.004 -1000
Canonical Wnt signaling pathway 32 1671 51 -0.15 0.09 1000 -1000 -0.037 -1000
Coregulation of Androgen receptor activity 31 2366 76 -0.15 0.054 1000 -1000 -0.02 -1000
Syndecan-2-mediated signaling events 30 2117 69 -0.019 0.047 1000 -1000 -0.03 -1000
Integrins in angiogenesis 30 2527 84 -0.12 0.058 1000 -1000 -0.033 -1000
E-cadherin signaling in the nascent adherens junction 30 2300 76 -0.081 0.056 1000 -1000 -0.05 -1000
Signaling events mediated by PTP1B 29 2278 76 -0.089 0.06 1000 -1000 -0.045 -1000
amb2 Integrin signaling 29 2382 82 -0.05 0.046 1000 -1000 -0.025 -1000
Caspase cascade in apoptosis 28 2125 74 -0.067 0.047 1000 -1000 -0.028 -1000
Cellular roles of Anthrax toxin 28 1125 39 -0.074 0.035 1000 -1000 -0.016 -1000
TCGA08_retinoblastoma 28 226 8 -0.011 0.023 1000 -1000 -0.005 -1000
VEGFR1 specific signals 28 1596 56 -0.028 0.036 1000 -1000 -0.021 -1000
Regulation of nuclear SMAD2/3 signaling 27 3688 136 -0.19 0.066 1000 -1000 -0.031 -1000
BMP receptor signaling 27 2212 81 -0.11 0.067 1000 -1000 -0.019 -1000
Visual signal transduction: Rods 27 1450 52 -0.066 0.065 1000 -1000 -0.014 -1000
Aurora B signaling 27 1844 67 -0.064 0.052 1000 -1000 -0.021 -1000
Nectin adhesion pathway 26 1690 63 -0.048 0.052 1000 -1000 -0.032 -1000
Reelin signaling pathway 26 1486 56 -0.071 0.068 1000 -1000 -0.025 -1000
IL1-mediated signaling events 25 1577 62 -0.028 0.075 1000 -1000 -0.025 -1000
BCR signaling pathway 24 2435 99 -0.1 0.064 1000 -1000 -0.057 -1000
PDGFR-alpha signaling pathway 23 1048 44 -0.14 0.049 1000 -1000 -0.023 -1000
mTOR signaling pathway 23 1222 53 -0.067 0.044 1000 -1000 -0.031 -1000
Arf6 downstream pathway 22 951 43 -0.047 0.048 1000 -1000 -0.03 -1000
PLK1 signaling events 22 1900 85 -0.073 0.051 1000 -1000 -0.03 -1000
S1P1 pathway 22 797 36 -0.034 0.036 1000 -1000 -0.02 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 22 990 45 -0.042 0.055 1000 -1000 -0.026 -1000
Visual signal transduction: Cones 21 824 38 -0.022 0.05 1000 -1000 0 -1000
Presenilin action in Notch and Wnt signaling 21 1314 61 -0.2 0.07 1000 -1000 -0.037 -1000
FOXA2 and FOXA3 transcription factor networks 21 986 46 -0.2 0.043 1000 -1000 -0.042 -1000
Glypican 1 network 21 1030 48 -0.023 0.049 1000 -1000 -0.021 -1000
Ceramide signaling pathway 20 1560 76 -0.069 0.068 1000 -1000 -0.019 -1000
TRAIL signaling pathway 20 1004 48 -0.024 0.036 1000 -1000 -0.017 -1000
Calcium signaling in the CD4+ TCR pathway 20 639 31 -0.035 0.045 1000 -1000 -0.04 -1000
Insulin Pathway 20 1548 74 -0.063 0.079 1000 -1000 -0.024 -1000
Class I PI3K signaling events 19 1457 73 -0.06 0.045 1000 -1000 -0.023 -1000
PDGFR-beta signaling pathway 19 1939 97 -0.066 0.066 1000 -1000 -0.031 -1000
ErbB2/ErbB3 signaling events 18 1198 65 -0.047 0.047 1000 -1000 -0.046 -1000
ceramide signaling pathway 18 905 49 -0.057 0.048 1000 -1000 -0.019 -1000
RXR and RAR heterodimerization with other nuclear receptor 18 939 52 -0.057 0.061 1000 -1000 -0.022 -1000
Regulation of Telomerase 18 1888 102 -0.15 0.062 1000 -1000 -0.031 -1000
Ras signaling in the CD4+ TCR pathway 18 313 17 -0.002 0.05 1000 -1000 -0.01 -1000
IFN-gamma pathway 17 1223 68 -0.058 0.059 1000 -1000 -0.042 -1000
EPHB forward signaling 17 1512 85 -0.046 0.11 1000 -1000 -0.047 -1000
Syndecan-3-mediated signaling events 16 572 35 -0.031 0.068 1000 -1000 -0.033 -1000
Hedgehog signaling events mediated by Gli proteins 15 1035 65 -0.024 0.076 1000 -1000 -0.021 -1000
p75(NTR)-mediated signaling 15 1942 125 -0.047 0.086 1000 -1000 -0.046 -1000
Atypical NF-kappaB pathway 15 488 31 -0.018 0.035 1000 -1000 -0.004 -1000
Signaling events mediated by VEGFR1 and VEGFR2 15 1911 125 -0.026 0.044 1000 -1000 -0.02 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 14 786 54 -0.036 0.049 1000 -1000 -0.017 -1000
EPO signaling pathway 14 822 55 -0.11 0.046 1000 -1000 -0.02 -1000
IL2 signaling events mediated by STAT5 14 311 22 -0.025 0.036 1000 -1000 -0.03 -1000
Neurotrophic factor-mediated Trk receptor signaling 14 1707 120 -0.079 0.088 1000 -1000 -0.032 -1000
Regulation of Androgen receptor activity 14 1011 70 -0.14 0.047 1000 -1000 -0.029 -1000
LPA4-mediated signaling events 13 162 12 -0.028 0.022 1000 -1000 -0.019 -1000
Sphingosine 1-phosphate (S1P) pathway 13 381 28 -0.01 0.043 1000 -1000 -0.003 -1000
Aurora A signaling 13 834 60 -0.011 0.05 1000 -1000 -0.011 -1000
HIF-2-alpha transcription factor network 13 601 43 -0.11 0.11 1000 -1000 -0.048 -1000
Retinoic acid receptors-mediated signaling 13 809 58 -0.071 0.067 1000 -1000 -0.027 -1000
Signaling mediated by p38-alpha and p38-beta 13 609 44 -0.054 0.056 1000 -1000 -0.004 -1000
Regulation of p38-alpha and p38-beta 13 753 54 -0.018 0.072 1000 -1000 -0.014 -1000
Glypican 2 network 13 54 4 0 0.013 1000 -1000 0 -1000
S1P4 pathway 13 329 25 -0.008 0.043 1000 -1000 -0.013 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 12 1072 85 -0.14 0.064 1000 -1000 -0.027 -1000
Effects of Botulinum toxin 12 316 26 -0.063 0.051 1000 -1000 0 -1000
S1P3 pathway 12 532 42 -0.017 0.043 1000 -1000 -0.021 -1000
p38 MAPK signaling pathway 12 555 44 -0.05 0.058 1000 -1000 -0.021 -1000
Paxillin-independent events mediated by a4b1 and a4b7 11 411 37 -0.024 0.073 1000 -1000 -0.022 -1000
S1P5 pathway 11 195 17 -0.001 0.035 1000 -1000 -0.007 -1000
FoxO family signaling 11 747 64 -0.092 0.048 1000 -1000 -0.033 -1000
Angiopoietin receptor Tie2-mediated signaling 11 998 88 -0.063 0.063 1000 -1000 -0.057 -1000
Nephrin/Neph1 signaling in the kidney podocyte 10 352 34 -0.039 0.076 1000 -1000 -0.029 -1000
BARD1 signaling events 10 604 57 -0.047 0.069 1000 -1000 -0.048 -1000
Signaling events mediated by HDAC Class III 10 407 40 -0.063 0.064 1000 -1000 -0.04 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 10 845 83 -0.057 0.069 1000 -1000 -0.014 -1000
Paxillin-dependent events mediated by a4b1 10 370 36 -0.061 0.064 1000 -1000 -0.034 -1000
TCGA08_rtk_signaling 10 272 26 -0.026 0.042 1000 -1000 -0.008 -1000
Signaling events mediated by PRL 10 357 34 -0.037 0.05 1000 -1000 -0.029 -1000
Signaling events mediated by HDAC Class II 9 689 75 -0.088 0.076 1000 -1000 -0.023 -1000
a4b1 and a4b7 Integrin signaling 9 47 5 0.021 0.041 1000 -1000 0.023 -1000
Class IB PI3K non-lipid kinase events 9 27 3 -0.025 0.025 1000 -1000 -0.023 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 8 285 33 -0.016 0.071 1000 -1000 -0.019 -1000
JNK signaling in the CD4+ TCR pathway 7 122 17 -0.01 0.078 1000 -1000 -0.019 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 6 141 23 0 0.054 1000 -1000 -0.015 -1000
Ephrin A reverse signaling 6 43 7 0 0.041 1000 -1000 0 -1000
Insulin-mediated glucose transport 6 209 32 0 0.043 1000 -1000 -0.012 -1000
Class I PI3K signaling events mediated by Akt 6 462 68 -0.053 0.075 1000 -1000 -0.019 -1000
Arf6 trafficking events 5 404 71 -0.04 0.042 1000 -1000 -0.024 -1000
Alternative NF-kappaB pathway 5 74 13 0 0.082 1000 -1000 0 -1000
Canonical NF-kappaB pathway 4 189 39 0 0.074 1000 -1000 -0.016 -1000
Circadian rhythm pathway 4 100 22 -0.01 0.066 1000 -1000 -0.024 -1000
Arf1 pathway 4 235 54 -0.001 0.06 1000 -1000 -0.009 -1000
Aurora C signaling 3 24 7 0 0.052 1000 -1000 -0.012 -1000
Signaling events mediated by HDAC Class I 3 370 104 -0.046 0.08 1000 -1000 -0.028 -1000
Rapid glucocorticoid signaling 2 56 20 -0.002 0.044 1000 -1000 0 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0 25 27 0 0.08 1000 -1000 -0.017 -1000
Total 3393 208678 7203 -11 7.9 131000 -131000 -3.3 -131000
+ Methods & Data