(Factor value) GROWTH_CONDITION/no co-culture
type: EFO_0000001
property type: GROWTH_CONDITION
property value: no co-culture

JOSD1
type: EnsemblDatabaseReference

224606_at
type: EFO_0005072
part of: A-AFFY-44

234192_s_at
type: EFO_0005072
part of: A-AFFY-44

JOSD1
type: EnsemblDatabaseReference

209184_s_at
type: EFO_0005072
part of: A-AFFY-44

(Assay) CLL_8_fresh
type: Assay
has participant: A-AFFY-44

CD180
type: EnsemblDatabaseReference

(Sample) cell type/B cell
type: CL_0000236
property type: cell type
property value: B cell

CLECL1 UP in 'co-culture with nurse-like cells' vs 'no co-culture'
type: IncreasedDifferentialExpressionRatio
fold change: 1.29337961111111
p value: 0.0346442820158598
refers to: 244413_at
refers to: CLECL1
t statistic: 5.32329261775108

CD180 UP in 'co-culture with nurse-like cells' vs 'no co-culture'
type: IncreasedDifferentialExpressionRatio
fold change: 1.54242411111111
p value: 0.0328818752794073
refers to: CD180
refers to: 206206_at
t statistic: 5.5779287474131

MAP1LC3B DOWN in 'co-culture with nurse-like cells' vs 'no co-culture'
type: DecreasedDifferentialExpressionRatio
fold change: -1.00624002222222
p value: 0.0346442820158598
refers to: MAP1LC3B
refers to: 239845_at
t statistic: -5.44621692770247

(Assay) CLL_9_14dNLC
type: Assay
has participant: A-AFFY-44

GKAP1 DOWN in 'co-culture with nurse-like cells' vs 'no co-culture'
type: DecreasedDifferentialExpressionRatio
fold change: -1.27572021111111
p value: 0.0403773632160859
refers to: 234192_s_at
refers to: GKAP1
t statistic: -5.05204625160356

CHPT1
type: EnsemblDatabaseReference

CHPT1
type: EnsemblDatabaseReference

A-AFFY-44
type: EFO_0000269

208621_s_at
type: EFO_0005072
part of: A-AFFY-44

221675_s_at
type: EFO_0005072
part of: A-AFFY-44

IRS2
type: EnsemblDatabaseReference

IRS2
type: EnsemblDatabaseReference

(Sample) individual/patient 6
type: EFO_0000001
property type: individual
property value: patient 6

208763_s_at
type: EFO_0005072
part of: A-AFFY-44

CLECL1
type: EnsemblDatabaseReference

CLECL1
type: EnsemblDatabaseReference

TSC22D3
type: EnsemblDatabaseReference

MAFF DOWN in 'co-culture with nurse-like cells' vs 'no co-culture'
type: DecreasedDifferentialExpressionRatio
fold change: -2.42039551111111
p value: 0.0457319620629129
refers to: 36711_at
refers to: MAFF
t statistic: -4.85562361733547

(Sample) individual/patient 5
type: EFO_0000001
property type: individual
property value: patient 5

(Assay) CLL_3_14dNLC
type: Assay
has participant: A-AFFY-44

KLF6 DOWN in 'co-culture with nurse-like cells' vs 'no co-culture'
type: DecreasedDifferentialExpressionRatio
fold change: -1.75398174444445
p value: 0.0359506155720139
refers to: 224606_at
refers to: KLF6
t statistic: -5.16284329343948

TSC22D3
type: EnsemblDatabaseReference

(Assay) CLL_2_14d_NLC
type: Assay
has participant: A-AFFY-44

204032_at
type: EFO_0005072
part of: A-AFFY-44

242458_at
type: EFO_0005072
part of: A-AFFY-44

(Sample) disease/chronic lymphocytic leukemia
type: EFO_0000095
property type: disease
property value: chronic lymphocytic leukemia

(Assay) CLL_7_fresh
type: Assay
has participant: A-AFFY-44

(Sample) individual/patient 1
type: EFO_0000001
property type: individual
property value: patient 1

(Factor value) GROWTH_CONDITION/co-culture with nurse-like cells
type: EFO_0000001
property type: GROWTH_CONDITION
property value: co-culture with nurse-like cells

(Assay) CLL_2_fresh
type: Assay
has participant: A-AFFY-44

RALGPS2
type: EnsemblDatabaseReference

239845_at
type: EFO_0005072
part of: A-AFFY-44

RALGPS2
type: EnsemblDatabaseReference

(Sample) individual/patient 7
type: EFO_0000001
property type: individual
property value: patient 7

CHPT1 DOWN in 'co-culture with nurse-like cells' vs 'no co-culture'
type: DecreasedDifferentialExpressionRatio
fold change: -1.41233294444445
p value: 0.0405768808595664
refers to: 221675_s_at
refers to: CHPT1
t statistic: -5.02362564079871

208622_s_at
type: EFO_0005072
part of: A-AFFY-44

(Assay) CLL_4_14dNLC
type: Assay
has participant: A-AFFY-44

(Assay) CLL_9_fresh
type: Assay
has participant: A-AFFY-44

244413_at
type: EFO_0005072
part of: A-AFFY-44

Homo sapiens
type: OBI_0100026

KLF6
type: EnsemblDatabaseReference

KLF6
type: EnsemblDatabaseReference

EZR DOWN in 'co-culture with nurse-like cells' vs 'no co-culture'
type: DecreasedDifferentialExpressionRatio
fold change: -1.06943538888889
p value: 0.0458320034821184
refers to: 208621_s_at
refers to: EZR
t statistic: -4.80073583222532

(Sample) individual/patient 9
type: EFO_0000001
property type: individual
property value: patient 9

MAFF
type: EnsemblDatabaseReference

(Assay) CLL_1_14dNLC
type: Assay
has participant: A-AFFY-44

MAFF
type: EnsemblDatabaseReference

EZR DOWN in 'co-culture with nurse-like cells' vs 'no co-culture'
type: DecreasedDifferentialExpressionRatio
fold change: -1.09483955555556
p value: 0.0471451980337352
refers to: EZR
refers to: 208622_s_at
t statistic: -4.7383805287098

(Sample) individual/patient 8
type: EFO_0000001
property type: individual
property value: patient 8

GKAP1
type: EnsemblDatabaseReference

E-GEOD-13811
type: microarray 1colour mrna differential
RO_0002162: Homo sapiens
description: In the marrow and lymphatic tissues, chronic lymphocytic leukemia (CLL) cells interact with accessory cells that constitute the leukemia microenvironment. In lymphatic tissues, CLL cells are interspersed with CD68+ nurselike cells (NLC) and T cells. However, the mechanism regulating co-localization of CLL cells and these accessory cells are largely unknown. To dissect the molecular cross-talk between CLL and NLC, we profiled the gene expression of CD19-purified CLL cells before and after co-culture with NLC. NLC co-culture induced high-level expression of B cell maturation antigen (BCMA) and two chemoattractants (CCL3, CCL4) by CLL cells. Supernatants from CLL-NLC co-cultures revealed high CCL3/CCL4 protein levels. B cell receptor triggering also induced a robust induction of CCL3 and CCL4 expression by CLL cells, which was almost completely abrogated by a specific Syc inhibitor, R406. High CCL3 and CCL4 plasma levels in CLL patients suggest that activation of this pathway plays a role in vivo. These studies reveal a novel mechanism of cross-talk between CLL cells and their microenvironment, namely the secretion of two T cell chemokines by CLL-NLC interaction and in response to BCR stimulation. Through these chemokines, CLL cells can recruit accessory cells, and thereby actively create a microenvironment that favors their growth and survival. Experiment Overall Design: The microarray part of this study included samples of CLL cells from 9 different patients, analyzed directly after purification and after 14 days of co-culture with Nurse like cells . Experiment Overall Design: In detail, RNA was isolated from CD19-purified CLL cells from 9 different patientsÃÂ¢ÃÂÃÂ peripheral blood mononuclear cells (PBMC) after Ficoll separation and subsequent purification with CD19 MicroBeads and the MACSÃÂÃÂ® technology according to the manufacturerÃÂ¢ÃÂÃÂs instructions (Miltenyi Biotec, Bergisch Gladbach, Germany). For comparison, the same CLL cell samples were co-cultured for 14…
uses data from: http://identifiers.org/pubmed/19074730

(Assay) CLL_7_14dNLC
type: Assay
has participant: A-AFFY-44

JOSD1 DOWN in 'co-culture with nurse-like cells' vs 'no co-culture'
type: DecreasedDifferentialExpressionRatio
fold change: -1.04518083333333
p value: 0.0359506155720139
refers to: 201751_at
refers to: JOSD1
t statistic: -5.18394719324452

BCAR3
type: EnsemblDatabaseReference

TSC22D3 DOWN in 'co-culture with nurse-like cells' vs 'no co-culture'
type: DecreasedDifferentialExpressionRatio
fold change: -2.38622252222222
p value: 0.0313363178820141
refers to: 208763_s_at
refers to: TSC22D3
t statistic: -6.21456999482517

(Sample) organism part/peripheral blood
type: UBERON_0000178
property type: organism part
property value: peripheral blood

(Assay) CLL_8_14dNLC
type: Assay
has participant: A-AFFY-44

(Assay) CLL_6_fresh
type: Assay
has participant: A-AFFY-44

(Sample) organism/Homo sapiens
type: Homo sapiens
property type: organism
property value: Homo sapiens

(Assay) CLL_5_fresh
type: Assay
has participant: A-AFFY-44

(Assay) CLL_6_14dNLC
type: Assay
has participant: A-AFFY-44

KLF6 DOWN in 'co-culture with nurse-like cells' vs 'no co-culture'
type: DecreasedDifferentialExpressionRatio
fold change: -1.79267732222222
p value: 0.0457319620629129
refers to: 1555832_s_at
refers to: KLF6
t statistic: -4.93841588808335

EZR
type: EnsemblDatabaseReference

EZR
type: EnsemblDatabaseReference

(Sample) individual/patient 2
type: EFO_0000001
property type: individual
property value: patient 2

207001_x_at
type: EFO_0005072
part of: A-AFFY-44

(Assay) CLL_5_14dNLC
type: Assay
has participant: A-AFFY-44

(Assay) CLL_4_fresh
type: Assay
has participant: A-AFFY-44

CD180
type: EnsemblDatabaseReference

GKAP1
type: EnsemblDatabaseReference

(Assay) CLL_3_fresh
type: Assay
has participant: A-AFFY-44

36711_at
type: EFO_0005072
part of: A-AFFY-44

(Sample) individual/patient 3
type: EFO_0000001
property type: individual
property value: patient 3

RALGPS2 UP in 'co-culture with nurse-like cells' vs 'no co-culture'
type: IncreasedDifferentialExpressionRatio
fold change: 1.07376905555555
p value: 0.0346442820158598
refers to: 242458_at
refers to: RALGPS2
t statistic: 5.37336278769462

1555832_s_at
type: EFO_0005072
part of: A-AFFY-44

TSC22D3 DOWN in 'co-culture with nurse-like cells' vs 'no co-culture'
type: DecreasedDifferentialExpressionRatio
fold change: -1.95099307777778
p value: 0.0346442820158598
refers to: TSC22D3
refers to: 207001_x_at
t statistic: -5.33842927896203

BCAR3
type: EnsemblDatabaseReference

Analysis of 'co-culture with nurse-like cells' vs 'no co-culture'
type: MicroarrayDifferentialExpressionAnalysis

(Sample) individual/patient 4
type: EFO_0000001
property type: individual
property value: patient 4

MAP1LC3B
type: EnsemblDatabaseReference

MAP1LC3B
type: EnsemblDatabaseReference

201751_at
type: EFO_0005072
part of: A-AFFY-44

IRS2 DOWN in 'co-culture with nurse-like cells' vs 'no co-culture'
type: DecreasedDifferentialExpressionRatio
fold change: -1.29445613333333
p value: 0.0471451980337352
refers to: IRS2
refers to: 209184_s_at
t statistic: -4.72317023926702

206206_at
type: EFO_0005072
part of: A-AFFY-44

BCAR3 UP in 'co-culture with nurse-like cells' vs 'no co-culture'
type: IncreasedDifferentialExpressionRatio
fold change: 1.383099
p value: 0.0471451980337352
refers to: 204032_at
refers to: BCAR3
t statistic: 4.72542705071932

(Assay) CLL_1_fresh
type: Assay
has participant: A-AFFY-44