Lung Squamous Cell Carcinoma: PARADIGM pathway analysis of mRNA expression data
Maintained by TCGA GDAC Team (Broad Institute/Dana-Farber Cancer Institute/Harvard Medical School)
- Overview
+ Introduction
- Summary

There were 62 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
TCGA08_retinoblastoma 53
HIF-1-alpha transcription factor network 35
Wnt signaling 26
IL23-mediated signaling events 26
IL4-mediated signaling events 23
TCGA08_p53 22
Noncanonical Wnt signaling pathway 21
Signaling mediated by p38-alpha and p38-beta 21
Syndecan-1-mediated signaling events 19
Glucocorticoid receptor regulatory network 19
- 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
TCGA08_retinoblastoma 53 429 8 -0.28 0.16 1000 -1000 -0.016 -1000
HIF-1-alpha transcription factor network 35 2674 76 -0.56 0.02 1000 -1000 -0.08 -1000
Wnt signaling 26 188 7 -0.2 -0.006 1000 -1000 -0.024 -1000
IL23-mediated signaling events 26 1605 60 -0.6 0.016 1000 -1000 -0.14 -1000
IL4-mediated signaling events 23 2104 91 -0.63 0.57 1000 -1000 -0.12 -1000
TCGA08_p53 22 155 7 -0.22 0.12 1000 -1000 -0.018 -1000
Noncanonical Wnt signaling pathway 21 557 26 -0.2 0.018 1000 -1000 -0.041 -1000
Signaling mediated by p38-alpha and p38-beta 21 924 44 -0.26 0.018 1000 -1000 -0.025 -1000
Syndecan-1-mediated signaling events 19 656 34 -0.24 0.018 1000 -1000 -0.037 -1000
Glucocorticoid receptor regulatory network 19 2215 114 -0.59 0.34 1000 -1000 -0.068 -1000
IL1-mediated signaling events 19 1184 62 -0.29 0.061 1000 -1000 -0.084 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 19 1330 68 -0.58 0.22 1000 -1000 -0.12 -1000
Fc-epsilon receptor I signaling in mast cells 18 1805 97 -0.2 0.044 1000 -1000 -0.09 -1000
Nectin adhesion pathway 18 1165 63 -0.21 0.028 1000 -1000 -0.076 -1000
Endothelins 18 1798 96 -0.31 0.018 1000 -1000 -0.071 -1000
BCR signaling pathway 18 1808 99 -0.26 0.028 1000 -1000 -0.091 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 18 1435 78 -0.23 0.1 1000 -1000 -0.061 -1000
Osteopontin-mediated events 17 675 38 -0.24 0.018 1000 -1000 -0.099 -1000
Signaling events mediated by the Hedgehog family 17 920 52 -0.3 0.1 1000 -1000 -0.038 -1000
Glypican 1 network 17 855 48 -0.12 0.078 1000 -1000 -0.034 -1000
EGFR-dependent Endothelin signaling events 17 362 21 -0.21 0.027 1000 -1000 -0.075 -1000
IL12-mediated signaling events 15 1342 87 -0.3 0.049 1000 -1000 -0.11 -1000
Calcium signaling in the CD4+ TCR pathway 15 493 31 -0.34 0.029 1000 -1000 -0.07 -1000
Syndecan-2-mediated signaling events 14 992 69 -0.24 0.018 1000 -1000 -0.028 -1000
Arf6 signaling events 14 886 62 -0.16 0.027 1000 -1000 -0.023 -1000
BMP receptor signaling 14 1172 81 -0.31 0.041 1000 -1000 -0.092 -1000
Ephrin B reverse signaling 14 713 48 -0.13 0.12 1000 -1000 -0.076 -1000
TCR signaling in naïve CD8+ T cells 14 1341 93 -0.14 0.027 1000 -1000 -0.074 -1000
IGF1 pathway 14 816 57 -0.13 0.063 1000 -1000 -0.097 -1000
Thromboxane A2 receptor signaling 13 1394 105 -0.18 0.046 1000 -1000 -0.072 -1000
amb2 Integrin signaling 13 1142 82 -0.19 0.018 1000 -1000 -0.079 -1000
EPHB forward signaling 13 1145 85 -0.16 0.14 1000 -1000 -0.096 -1000
Syndecan-4-mediated signaling events 13 884 67 -0.12 0.018 1000 -1000 -0.085 -1000
PLK2 and PLK4 events 12 36 3 -0.051 0.015 1000 -1000 -0.016 -1000
FAS signaling pathway (CD95) 12 569 47 -0.21 0.036 1000 -1000 -0.037 -1000
IL27-mediated signaling events 12 628 51 -0.31 0.15 1000 -1000 -0.088 -1000
FOXM1 transcription factor network 12 638 51 -0.32 0.073 1000 -1000 -0.14 -1000
FOXA2 and FOXA3 transcription factor networks 11 514 46 -0.15 0.032 1000 -1000 -0.036 -1000
PDGFR-alpha signaling pathway 11 497 44 -0.2 0.033 1000 -1000 -0.061 -1000
TRAIL signaling pathway 11 537 48 -0.087 0.018 1000 -1000 -0.072 -1000
S1P1 pathway 11 404 36 -0.24 0.018 1000 -1000 -0.082 -1000
Syndecan-3-mediated signaling events 11 418 35 -0.26 0.031 1000 -1000 -0.032 -1000
LPA receptor mediated events 11 1179 102 -0.25 0.036 1000 -1000 -0.078 -1000
IL6-mediated signaling events 11 840 75 -0.15 0.04 1000 -1000 -0.078 -1000
Glypican 2 network 10 42 4 -0.037 0 1000 -1000 -0.018 -1000
E-cadherin signaling events 10 54 5 -0.034 0.008 1000 -1000 -0.02 -1000
p75(NTR)-mediated signaling 9 1238 125 -0.27 0.031 1000 -1000 -0.092 -1000
Integrins in angiogenesis 9 771 84 -0.22 0.027 1000 -1000 -0.097 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 9 416 45 -0.14 0.028 1000 -1000 -0.087 -1000
Canonical Wnt signaling pathway 9 482 51 -0.28 0.08 1000 -1000 -0.057 -1000
Caspase cascade in apoptosis 8 626 74 -0.095 0.048 1000 -1000 -0.031 -1000
Coregulation of Androgen receptor activity 8 645 76 -0.29 0.043 1000 -1000 -0.037 -1000
Visual signal transduction: Cones 8 339 38 -0.1 0.021 1000 -1000 -0.059 -1000
Signaling events mediated by PTP1B 8 679 76 -0.16 0.074 1000 -1000 -0.082 -1000
Presenilin action in Notch and Wnt signaling 8 533 61 -0.28 0.035 1000 -1000 -0.082 -1000
IFN-gamma pathway 8 605 68 -0.21 0.021 1000 -1000 -0.089 -1000
HIF-2-alpha transcription factor network 8 373 43 -0.16 0.029 1000 -1000 -0.067 -1000
Nongenotropic Androgen signaling 8 445 52 -0.078 0.024 1000 -1000 -0.068 -1000
Stabilization and expansion of the E-cadherin adherens junction 8 661 74 -0.17 0.035 1000 -1000 -0.095 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 8 274 33 -0.29 0.037 1000 -1000 -0.033 -1000
E-cadherin signaling in keratinocytes 8 347 43 -0.093 0.018 1000 -1000 -0.076 -1000
Ras signaling in the CD4+ TCR pathway 8 147 17 -0.059 0.016 1000 -1000 -0.042 -1000
ErbB4 signaling events 7 516 69 -0.15 0.036 1000 -1000 -0.1 -1000
Sphingosine 1-phosphate (S1P) pathway 7 205 28 -0.097 0.022 1000 -1000 -0.025 -1000
Ephrin A reverse signaling 7 51 7 -0.017 0.015 1000 -1000 -0.008 -1000
Cellular roles of Anthrax toxin 7 292 39 -0.081 0.018 1000 -1000 -0.033 -1000
Arf6 downstream pathway 7 333 43 -0.049 0.023 1000 -1000 -0.04 -1000
Reelin signaling pathway 7 433 56 -0.15 0.041 1000 -1000 -0.085 -1000
IL2 signaling events mediated by STAT5 7 167 22 -0.11 0.032 1000 -1000 -0.044 -1000
Plasma membrane estrogen receptor signaling 7 658 86 -0.12 0.035 1000 -1000 -0.094 -1000
VEGFR1 specific signals 7 425 56 -0.086 0.018 1000 -1000 -0.052 -1000
Neurotrophic factor-mediated Trk receptor signaling 7 893 120 -0.24 0.11 1000 -1000 -0.082 -1000
Visual signal transduction: Rods 7 389 52 -0.15 0.023 1000 -1000 -0.092 -1000
LPA4-mediated signaling events 6 79 12 -0.038 0.025 1000 -1000 -0.02 -1000
Regulation of nuclear SMAD2/3 signaling 6 935 136 -0.32 0.12 1000 -1000 -0.068 -1000
Hedgehog signaling events mediated by Gli proteins 6 426 65 -0.25 0.048 1000 -1000 -0.059 -1000
Ceramide signaling pathway 6 528 76 -0.13 0.052 1000 -1000 -0.031 -1000
Signaling mediated by p38-gamma and p38-delta 6 95 15 -0.048 0.018 1000 -1000 -0.024 -1000
IL2 signaling events mediated by PI3K 6 379 58 -0.13 0.021 1000 -1000 -0.08 -1000
Signaling events mediated by VEGFR1 and VEGFR2 6 854 125 -0.092 0.04 1000 -1000 -0.11 -1000
TCGA08_rtk_signaling 6 164 26 -0.093 0.032 1000 -1000 -0.016 -1000
Class I PI3K signaling events 6 443 73 -0.052 0.033 1000 -1000 -0.057 -1000
Regulation of Telomerase 6 614 102 -0.21 0.057 1000 -1000 -0.1 -1000
Regulation of Androgen receptor activity 6 442 70 -0.4 0.047 1000 -1000 -0.069 -1000
a4b1 and a4b7 Integrin signaling 5 29 5 -0.013 0.018 1000 -1000 -0.015 -1000
Signaling events mediated by HDAC Class III 5 238 40 -0.13 0.034 1000 -1000 -0.03 -1000
RXR and RAR heterodimerization with other nuclear receptor 5 264 52 -0.079 0.048 1000 -1000 -0.045 -1000
Retinoic acid receptors-mediated signaling 5 291 58 -0.11 0.036 1000 -1000 -0.081 -1000
Atypical NF-kappaB pathway 5 162 31 -0.039 0.034 1000 -1000 -0.019 -1000
E-cadherin signaling in the nascent adherens junction 5 403 76 -0.089 0.031 1000 -1000 -0.084 -1000
Insulin Pathway 5 389 74 -0.11 0.057 1000 -1000 -0.094 -1000
Angiopoietin receptor Tie2-mediated signaling 5 461 88 -0.11 0.056 1000 -1000 -0.097 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 4 264 54 -0.11 0.038 1000 -1000 -0.095 -1000
JNK signaling in the CD4+ TCR pathway 4 76 17 -0.058 0.021 1000 -1000 -0.036 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 4 380 85 -0.11 0.046 1000 -1000 -0.074 -1000
mTOR signaling pathway 4 222 53 -0.043 0.035 1000 -1000 -0.059 -1000
Paxillin-independent events mediated by a4b1 and a4b7 4 183 37 -0.053 0.027 1000 -1000 -0.052 -1000
ceramide signaling pathway 4 223 49 -0.095 0.033 1000 -1000 -0.04 -1000
FoxO family signaling 4 276 64 -0.14 0.11 1000 -1000 -0.058 -1000
Paxillin-dependent events mediated by a4b1 4 147 36 -0.053 0.037 1000 -1000 -0.075 -1000
S1P3 pathway 4 197 42 -0.05 0.022 1000 -1000 -0.033 -1000
PDGFR-beta signaling pathway 4 390 97 -0.087 0.048 1000 -1000 -0.088 -1000
Signaling events mediated by PRL 4 141 34 -0.054 0.027 1000 -1000 -0.04 -1000
Class IB PI3K non-lipid kinase events 4 12 3 -0.005 0.005 1000 -1000 -0.009 -1000
Aurora B signaling 4 298 67 -0.18 0.033 1000 -1000 -0.079 -1000
ErbB2/ErbB3 signaling events 3 233 65 -0.064 0.039 1000 -1000 -0.077 -1000
Aurora A signaling 3 221 60 -0.046 0.04 1000 -1000 -0.029 -1000
Signaling events regulated by Ret tyrosine kinase 3 315 82 -0.12 0.036 1000 -1000 -0.092 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 3 271 83 -0.076 0.056 1000 -1000 -0.077 -1000
Regulation of p38-alpha and p38-beta 3 188 54 -0.039 0.039 1000 -1000 -0.056 -1000
Effects of Botulinum toxin 3 101 26 -0.067 0.02 1000 -1000 -0.061 -1000
Arf6 trafficking events 3 283 71 -0.045 0.042 1000 -1000 -0.078 -1000
p38 MAPK signaling pathway 3 153 44 -0.023 0.031 1000 -1000 -0.074 -1000
Canonical NF-kappaB pathway 2 106 39 -0.063 0.074 1000 -1000 -0.092 -1000
Circadian rhythm pathway 2 53 22 -0.016 0.04 1000 -1000 -0.039 -1000
EPO signaling pathway 2 145 55 -0.044 0.045 1000 -1000 -0.09 -1000
PLK1 signaling events 2 173 85 -0.032 0.042 1000 -1000 -0.055 -1000
Insulin-mediated glucose transport 2 82 32 -0.057 0.03 1000 -1000 -0.026 -1000
Class I PI3K signaling events mediated by Akt 2 169 68 -0.057 0.059 1000 -1000 -0.06 -1000
S1P5 pathway 2 38 17 -0.032 0.018 1000 -1000 -0.026 -1000
Rapid glucocorticoid signaling 2 55 20 -0.035 0.025 1000 -1000 -0.02 -1000
S1P4 pathway 2 54 25 -0.032 0.027 1000 -1000 -0.025 -1000
Alternative NF-kappaB pathway 2 26 13 -0.004 0.036 1000 -1000 -0.031 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 1 35 23 -0.003 0.037 1000 -1000 -0.039 -1000
Nephrin/Neph1 signaling in the kidney podocyte 1 42 34 -0.018 0.04 1000 -1000 -0.035 -1000
Signaling events mediated by HDAC Class II 1 144 75 -0.05 0.043 1000 -1000 -0.049 -1000
BARD1 signaling events 1 106 57 -0.027 0.051 1000 -1000 -0.038 -1000
Signaling events mediated by HDAC Class I 1 145 104 -0.037 0.065 1000 -1000 -0.068 -1000
Aurora C signaling 0 5 7 -0.002 0.028 1000 -1000 -0.036 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0 20 27 -0.006 0.042 1000 -1000 -0.057 -1000
Arf1 pathway 0 39 54 -0.007 0.034 1000 -1000 -0.034 -1000
Total 1188 69670 7203 -20 6.3 131000 -131000 -8 -131000
+ Methods & Data
+ Meta