Details for: LINC01844

Gene ID: 101926975

Gene Type:  ncRNA (Non-coding RNA)  - A functional RNA molecule that is transcribed from DNA but not translated into a protein. Includes classes like miRNA and lncRNA.

Symbol: LINC01844

Ensembl ID: ENSG00000231185

Description: long intergenic non-protein coding RNA 1844

Selected Context(s):  Overall

Cell Significance Landscape

Contexts:

Significant Cells

Cell Significance Index (CSI) scores for the chosen context(s)

  • choroid plexus epithelial cell CL0000706
    CSI 13.36
    rCSI 21.88%
    PRS 88.63
  • alveolar type 1 fibroblast cell CL4028004
    CSI 13.15
    rCSI 14.4%
    PRS 95.1
  • retinal pigment epithelial cell CL0002586
    CSI 10.73
    rCSI 21.3%
    PRS 91.11
  • glioblast CL0000030
    CSI 9.74
    rCSI 15.53%
    PRS 87.79
  • retinal cone cell CL0000573
    CSI 9.4
    rCSI 15.14%
    PRS 87.52
  • pulmonary alveolar type 2 cell CL0002063
    CSI 7.34
    rCSI 11.39%
    PRS 94.27
  • amacrine cell CL0000561
    CSI 7.31
    rCSI 21.2%
    PRS 87.36
  • S cone cell CL0003050
    CSI 6.8
    rCSI 29.87%
    PRS 90.47
  • retinal rod cell CL0000604
    CSI 6.79
    rCSI 11.96%
    PRS 90.47
  • sst GABAergic cortical interneuron CL4023017
    CSI 6.67
    rCSI 8.6%
    PRS 85.29
  • inhibitory interneuron CL0000498
    CSI 6.49
    rCSI 14.97%
    PRS 86.99
  • blood vessel endothelial cell CL0000071
    CSI 5.87
    rCSI 12.19%
    PRS 92.45
  • mural cell CL0008034
    CSI 5.85
    rCSI 19.81%
    PRS 89.9
  • adipocyte CL0000136
    CSI 5.78
    rCSI 7.43%
    PRS 87.21
  • chondrocyte CL0000138
    CSI 5.05
    rCSI 8.03%
    PRS 90.44
  • interstitial cell of Cajal CL0002088
    CSI 4.8
    rCSI 6.11%
    PRS 96.19
  • diffuse bipolar 3a cell CL4033029
    CSI 4.59
    rCSI 31.24%
    PRS 86.82
  • Mueller cell CL0000636
    CSI 4.47
    rCSI 10.2%
    PRS 88.78
  • Schwann cell CL0002573
    CSI 4.4
    rCSI 12.51%
    PRS 90.94
  • lamp5 GABAergic cortical interneuron CL4023011
    CSI 4.17
    rCSI 7%
    PRS 84.45
  • rod bipolar cell CL0000751
    CSI 4.06
    rCSI 7.29%
    PRS 90.09
  • neuron CL0000540
    CSI 3.86
    rCSI 10.27%
    PRS 83.67
  • hepatic stellate cell CL0000632
    CSI 3.79
    rCSI 14.19%
    PRS 90.94
  • subcutaneous adipocyte CL0002521
    CSI 3.72
    rCSI 19.07%
    PRS 94.93
  • epicardial adipocyte CL1000309
    CSI 3.66
    rCSI 11.92%
    PRS 91.59
  • interneuron CL0000099
    CSI 3.36
    rCSI 6.75%
    PRS 89.44
  • vascular leptomeningeal cell CL4023051
    CSI 3.29
    rCSI 5.76%
    PRS 91.59
  • retinal bipolar neuron CL0000748
    CSI 3.12
    rCSI 5.84%
    PRS 87.51
  • Bergmann glial cell CL0000644
    CSI 2.97
    rCSI 4.06%
    PRS 88.01
  • pvalb GABAergic cortical interneuron CL4023018
    CSI 2.89
    rCSI 3.59%
    PRS 82.24
  • kidney loop of Henle thin descending limb epithelial cell CL1001111
    CSI 2.86
    rCSI 4.06%
    PRS 92.52
  • glutamatergic neuron CL0000679
    CSI 2.84
    rCSI 5.84%
    PRS 84.25
  • lung pericyte CL0009089
    CSI 2.75
    rCSI 7.25%
    PRS 96.5
  • retinal ganglion cell CL0000740
    CSI 2.68
    rCSI 5.92%
    PRS 85.83
  • differentiation-committed oligodendrocyte precursor CL4023059
    CSI 2.59
    rCSI 4.71%
    PRS 89.06
  • kidney connecting tubule epithelial cell CL1000768
    CSI 2.56
    rCSI 6.5%
    PRS 89.91
  • regular atrial cardiac myocyte CL0002129
    CSI 2.52
    rCSI 8.1%
    PRS 90.72
  • GABAergic neuron CL0000617
    CSI 2.42
    rCSI 8.1%
    PRS 83.09
  • fibroblast of cardiac tissue CL0002548
    CSI 2.4
    rCSI 11.5%
    PRS 94.58
  • cardiac muscle cell CL0000746
    CSI 2.27
    rCSI 3.26%
    PRS 87.34
  • VIP GABAergic cortical interneuron CL4023016
    CSI 2.23
    rCSI 2.66%
    PRS 84.35
  • mesothelial cell CL0000077
    CSI 2.06
    rCSI 8.06%
    PRS 81.22
  • regular ventricular cardiac myocyte CL0002131
    CSI 2.01
    rCSI 12.57%
    PRS 88.72
  • chandelier pvalb GABAergic cortical interneuron CL4023036
    CSI 1.98
    rCSI 6.19%
    PRS 87.07
  • L5 extratelencephalic projecting glutamatergic cortical neuron CL4023041
    CSI 1.96
    rCSI 7.07%
    PRS 82.54
  • macroglial cell CL0000126
    CSI 1.96
    rCSI 5.04%
    PRS 90.59
  • renal interstitial pericyte CL1001318
    CSI 1.88
    rCSI 5.17%
    PRS 92.3
  • cardiac neuron CL0010022
    CSI 1.85
    rCSI 5.9%
    PRS 92.92
  • renal principal cell CL0005009
    CSI 1.8
    rCSI 4.68%
    PRS 93.53
  • GABAergic amacrine cell CL4030027
    CSI 1.73
    rCSI 5.91%
    PRS 83.57
  • contractile cell CL0000183
    CSI 1.69
    rCSI 4.99%
    PRS 93.39
  • L6b glutamatergic cortical neuron CL4023038
    CSI 1.54
    rCSI 4.83%
    PRS 85.31
  • mesangial cell CL0000650
    CSI 1.33
    rCSI 5.42%
    PRS 96.83
  • L4 intratelencephalic projecting glutamatergic neuron CL4030063
    CSI 1.29
    rCSI 3.08%
    PRS 85.75
  • near-projecting glutamatergic cortical neuron CL4023012
    CSI 1.23
    rCSI 4.66%
    PRS 84.51
  • glial cell CL0000125
    CSI 1.03
    rCSI 3.91%
    PRS 88.49
  • flat midget bipolar cell CL4033033
    CSI 0.93
    rCSI 6.67%
    PRS 85.83
  • L2/3-6 intratelencephalic projecting glutamatergic neuron CL4023040
    CSI 0.83
    rCSI 2.02%
    PRS 82.26
  • diffuse bipolar 2 cell CL4033028
    CSI 0.81
    rCSI 6.24%
    PRS 87.44
  • podocyte CL0000653
    CSI 0.68
    rCSI 3.01%
    PRS 93.94
  • ON parasol ganglion cell CL4033052
    CSI 0.56
    rCSI 7.98%
    PRS 87.74
  • blood vessel smooth muscle cell CL0019018
    CSI 0.52
    rCSI 4.22%
    PRS 92.48
  • corticothalamic-projecting glutamatergic cortical neuron CL4023013
    CSI 0.47
    rCSI 2.77%
    PRS 84.69

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this specific cell.

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this cell type. Calculated using techniques like effect size estimation and bootstrapping for reliability.

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this cell type. Calculated using techniques like effect size estimation and bootstrapping for reliability.
Network Configuration

Explore relationships of the current gene. Select an Interaction Source: 'ONTOLOGY' for shared pathways (GO/Reactome) or 'STRING' for protein-protein interactions. Further refine by selecting context genes and comparing Cell Significance Index (CSI) scores between baseline and target cell types and their specific contexts.

Comma-separated if multiple.
Comma-separated if multiple.
Legend:
  • Query Gene
  • Node Color (Target Cell CSI, relative to current network):
    • Very High
    • High
    • Medium
    • Low
    • Very Low
    • CSI N/A
  • Node Size: Proportional to Target Cell CSI magnitude
  • STRING PPI Edge
  • Shared Pathway Edge (ONTOLOGY)

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Other Information

This section provides additional information about the gene, including a description generated by an AI language model and details about associated proteins.

## Summary [LINC01844](/details-gene/101926975) is a long intergenic non-protein coding RNA (lncRNA) located on human chromosome 5q31.3. As a non-coding transcript, its function is likely regulatory in nature. **Overall**, expression data reveals that [LINC01844](/details-gene/101926975) is a highly specific marker for a distinct set of specialized cell types, primarily within the central nervous system, eye, and lung. Its most significant expression is observed in [choroid plexus epithelial cells](/details-cell/CL0000706), [alveolar type 1 fibroblast cells](/details-cell/CL4028004), and various retinal cells, including [retinal pigment epithelial cells](/details-cell/CL0002586). The notable presence of this lncRNA in these functionally diverse but highly specialized cell populations, including the malignant [glioblast](/details-cell/CL0000030), suggests a potential role in cellular identity, barrier function, and possibly oncogenesis. ## Cellular Roles and Expression Landscape The expression profile of [LINC01844](/details-gene/101926975) indicates a highly specialized, rather than a ubiquitous, function. The gene's significance is highest in cells that constitute critical biological barriers or perform unique physiological roles. **Overall**, the gene's primary expression domains can be grouped into several functional categories: * **Neuro-ocular Tissues:** [LINC01844](/details-gene/101926975) demonstrates prominent significance in cells of the central nervous system and the eye. It is the top marker in [choroid plexus epithelial cells](/details-cell/CL0000706), which form the blood-cerebrospinal fluid barrier. It is also highly significant in multiple retinal cell types, including the [retinal pigment epithelial cells](/details-cell/CL0002586) that form the outer blood-retina barrier, as well as photoreceptor cells such as [retinal cone cells](/details-cell/CL0000573) and [retinal rod cells](/details-cell/CL0000604). Its high CSI in neuronal subtypes like [amacrine cells](/details-cell/CL0000561) and [sst GABAergic cortical interneurons](/details-cell/CL4023017) further reinforces its specific role in the nervous system. * **Pulmonary Tissues:** The lncRNA is a defining feature of the lung parenchyma, showing exceptionally high significance in [alveolar type 1 fibroblast cells](/details-cell/CL4028004) and a strong signal in [pulmonary alveolar type 2 cells](/details-cell/CL0002063). This pattern suggests a role in maintaining the structural integrity or functional capacity of the lung's gas-exchange units. * **Cancer Context:** A notable finding is the high significance of [LINC01844](/details-gene/101926975) in [glioblasts](/details-cell/CL0000030), a type of malignant brain tumor cell. This suggests that the regulatory functions of this lncRNA may be co-opted or dysregulated during gliomagenesis. * **Mesenchymal and Vascular Tissues:** While at lower CSI values, the gene also shows relevance in a range of other cell types, including [blood vessel endothelial cells](/details-cell/CL0000071), [mural cells](/details-cell/CL0008034), [adipocytes](/details-cell/CL0000136), and [chondrocytes](/details-cell/CL0000138), indicating a broader, albeit less prominent, role in various connective and vascular tissues. The highly specific expression pattern across these distinct lineages suggests that [LINC01844](/details-gene/101926975) is likely involved in executing or maintaining cell-type-specific transcriptional programs. ## Pathways and Molecular Function The precise molecular function of [LINC01844](/details-gene/101926975) remains to be elucidated, as is common for lncRNAs. Functional annotations are currently limited. However, its cell-specific expression landscape allows for informed inference about its potential biological roles. * Given its high significance in [choroid plexus epithelial cells](/details-cell/CL0000706) and [retinal pigment epithelial cells](/details-cell/CL0002586), [LINC01844](/details-gene/101926975) may be involved in regulating the expression of genes critical for establishing and maintaining the blood-brain and blood-retina barriers, such as those encoding tight junction proteins or specialized transporters. * Its expression in photoreceptors ([retinal cone cell](/details-cell/CL0000573), [retinal rod cell](/details-cell/CL0000604)) and interneurons ([amacrine cell](/details-cell/CL0000561)) points towards a potential function in neuronal differentiation, survival, or the regulation of phototransduction pathways. * In the lung, its prominence in alveolar cells suggests a role in pathways related to extracellular matrix production by fibroblasts, alveolar-capillary barrier function, or the synthesis and secretion of pulmonary surfactant by type 2 cells. As a lncRNA, [LINC01844](/details-gene/101926975) could exert its function by acting as a molecular scaffold for protein complexes, as a decoy for microRNAs, or by directly guiding chromatin-modifying enzymes to target gene promoters to regulate transcription. ## Research Directions The specific expression pattern of [LINC01844](/details-gene/101926975), particularly its high significance in both specialized healthy cells and a malignant cell type, provides a foundation for several compelling research avenues. ### Proposed Hypotheses: 1. **[LINC01844](/details-gene/101926975) functions as an oncogenic lncRNA in glioblastoma.** Its high expression in [glioblasts](/details-cell/CL0000030) may promote tumor cell proliferation, survival, or invasion by dysregulating gene networks that are normally active in its native neural or epithelial contexts. 2. **[LINC01844](/details-gene/101926975) is a key transcriptional regulator of blood-CNS barrier integrity.** Its top-ranking expression in [choroid plexus epithelial cells](/details-cell/CL0000706) suggests it is essential for the formation or maintenance of the blood-cerebrospinal fluid barrier, potentially by controlling the expression of cell adhesion molecules. 3. **[LINC01844](/details-gene/101926975) plays a role in the terminal differentiation and function of retinal photoreceptors.** Its high significance in both [retinal cone cells](/details-cell/CL0000573) and [retinal rod cells](/details-cell/CL0000604) implies it could be involved in regulating the expression of opsins or other proteins critical for phototransduction. ### Suggested Experimental Approach: To test the hypothesis that **[LINC01844](/details-gene/101926975) acts as an oncogene in glioblastoma**, a loss-of-function study could be conducted. One could use CRISPR interference (CRISPRi) or antisense oligonucleotides (ASOs) to specifically knockdown [LINC01844](/details-gene/101926975) in patient-derived [glioblast](/details-cell/CL0000030) cell lines. The consequences of its depletion on key cancer hallmarks, such as proliferation (via cell counting or colony formation assays), apoptosis (via TUNEL or Annexin V staining), and invasion (via Matrigel transwell assays), would be quantified. Subsequent RNA-sequencing of the knockdown cells could then identify the downstream transcriptional programs regulated by this lncRNA, providing mechanistic insight into its pro-tumorigenic role. ### Therapeutic Potential: Given its high and specific expression in [glioblasts](/details-cell/CL0000030), [LINC01844](/details-gene/101926975) represents a potential therapeutic target. A therapeutic strategy would focus on **inhibition** of its function. Since lncRNAs are not easily targeted by small molecule inhibitors, nucleic acid-based therapeutics, such as ASOs or siRNAs delivered via lipid nanoparticles, would be the most promising approach. The primary challenge would be ensuring specific delivery to the brain tumor while minimizing off-target effects in healthy cells where [LINC01844](/details-gene/101926975) is also highly expressed, such as the choroid plexus and retina, which would require careful toxicological evaluation.