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Analysis Pipeline

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Selection criteria for significant gene list :: Significant genes are selected with a p value cut-off of 0.1. The resultant list was then sorted in a descending order of fold change value. From the sorted list, the top 100 genes were selected for pathway/network. If the gene list is less than 100, the entire gene list was taken for pathway/network analysis.

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>>Total hits : 92 , Search term given : Nervous AND System Neoplasms

Patched heterozygous model of medulloblastoma

GEO Description :
Analysis of granule cell precursors, pre-neoplastic cells, and tumor cells obtained from 7 day old, 6 week old, and 10 to 25 week old patched heterozygous animals, respectively. Results provide insight into the mechanisms of pathogenesis of medulloblastoma at the early stage.
Organism : Mus musculus
GEO-ID : GDS1110

Compared Group :
tumor cell Vs pre-neoplastic cell

Number of Nodes in the Network : 38
Number of Nodes passing Cut-Off : 100
PValue Cut-Off : 2.21528807742288e-05
Fold Change Cut-Off : 2.17

Compared Group :
granule cell precursor Vs pre-neoplastic cell

Number of Nodes in the Network : 25
Number of Nodes passing Cut-Off : 100
PValue Cut-Off : 1.74339413661073e-06
Fold Change Cut-Off : 2.55

Compared Group :
tumor cell Vs granule cell precursor

Number of Nodes in the Network : 40
Number of Nodes passing Cut-Off : 100
PValue Cut-Off : 2.63512310993974e-06
Fold Change Cut-Off : 2.31

Neurofibromatosis and neurodevelopment

GEO Description :
Examination of hippocampus from 10 to 32 day old NF1 heterozygotes. NF1+/- mice develop learning and memory difficulties mimicking cognitive deficits in human neurofibromatosis.
Organism : Mus musculus
GEO-ID : GDS604

Compared Group :
18 d Vs 28 d

Number of Nodes in the Network : 31
Number of Nodes passing Cut-Off : 99
PValue Cut-Off : 0.000880349543876946
Fold Change Cut-Off : 2.24

Renin-angiotensin system inhibition effect on cerebral capillaries

GEO Description :
Examination of cerebral capillaries in stroke-prone spontaneously hypertensives (SHRSP) treated with either an angiotensin II receptor (AT1R) antagonist or an angiotensin converting enzyme (ACE) inhibitor. Renin-angiotensin system inhibition reduces stroke in SHRSP.
Organism : Rattus norvegicus
GEO-ID : GDS726

Compared Group :
control Vs lisinopril (ACE)

Number of Nodes in the Network : 14
Number of Nodes passing Cut-Off : 51
PValue Cut-Off : 0.000807550852186978
Fold Change Cut-Off : 2.25

Spinal cord injury and regeneration time course: above T9 (RG-U34A)

GEO Description :
Temporal analysis of molecular mechanisms of spinal cord degeneration and repair. Analyzed spinal cord above thoracic vertebrae T9 at various time points up to 28 days post injury. Mild, moderate and severe injury examined.
Organism : Rattus norvegicus
GEO-ID : GDS872

Compared Group :
control Vs moderate injury

Number of Nodes in the Network : 48
Number of Nodes passing Cut-Off : 100
PValue Cut-Off : 5.00889001386895e-08
Fold Change Cut-Off : 2.3

Spinal cord injury and regeneration time course: above T9 (RG-U34B)

GEO Description :
Temporal analysis of molecular mechanisms of spinal cord degeneration and repair. Analyzed spinal cord above thoracic vertebrae T9 at various time points up to 28 days post injury. Mild and severe injury examined.
Organism : Rattus norvegicus
GEO-ID : GDS873

Compared Group :
control Vs mild injury

Number of Nodes in the Network : 8
Number of Nodes passing Cut-Off : 100
PValue Cut-Off : 3.63207145710476e-05
Fold Change Cut-Off : 2.06

Angiotensin II type 1 receptor antagonist effect on brain microvessels of hypertensive animals

GEO Description :
Analysis of brain microvessels from hypertensive SHR males treated with candesartan, an angiotensin II type 1 receptor (AT1) antagonist, daily for 4 weeks. Blockade of angiotensin II AT1 receptors in cerebral microvessels protects against brain ischemia and inflammation.
Organism : Rattus norvegicus
GEO-ID : GDS2070

Compared Group :
control Vs candesartan

Number of Nodes in the Network : 42
Number of Nodes passing Cut-Off : 100
PValue Cut-Off : 1.94917652152071e-06
Fold Change Cut-Off : 2.21

Brain trauma model: time course (RG-U34A)

GEO Description :
Analysis of brain at various time points up to 21 days following lateral fluid percussion-induced brain injury. Delayed cell death following trauma results in brain damage. Results provide insight into the mechanisms underlying brain damage after traumatic injury.
Organism : Rattus norvegicus
GEO-ID : GDS2851

Compared Group :
sham Vs lateral fluid percussion-induced injury

Number of Nodes in the Network : 48
Number of Nodes passing Cut-Off : 100
PValue Cut-Off : 0.000165592311532237
Fold Change Cut-Off : 2.08

Spinal cord injury and regeneration time course: at T9 (RG-U34C)

GEO Description :
Temporal analysis of molecular mechanisms of spinal cord degeneration and repair. Analyzed spinal cord at thoracic vertebrae T9 at various time points up to 28 days post injury. Mild, moderate and severe injury examined.
Organism : Rattus norvegicus
GEO-ID : GDS339

Compared Group :
control Vs moderate injury

Number of Nodes in the Network : 8
Number of Nodes passing Cut-Off : 100
PValue Cut-Off : 2.11015441231588e-11
Fold Change Cut-Off : 2.32

DISCLAIMER:
The interactions, networks, list of genes/molecules or any other information presented here, is HYPOTHETICAL in nature and is based on information collected from public as well as other sources, and is analyzed by certain automated mining and analysis software workflows. Strandlife Science Pvt.Ltd. or the Editors of PathwayWorld offer this information with NO CLAIMS of accuracy and WARRANTIES of any kind, and DO NOT Accept liability or legal responsibility for losses allegedly caused by using this information.

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