Siftome Phase 3L

GSE159330

Expression profiling by small RNA-seq for identifying miRNAs associated with pathological classifications in thyroid cancer.

Not suitable Dataset does not meet the current suitability threshold.
Sample grouping CSV Contrast CSV DESeq2 metadata CSV R handoff notes Handoff report Download instructions Open GEO dataset
Source
GEO
Search intent
Patient tissue tumor-vs-normal
Intent behavior
search-intent-behavior-v1
Submission date
2020-10-09
Last update
2021-03-03
Organization
Korea Research Institutue of Bioscience & Biotechnology
Department
Personalized Genomic Medicine Research Center
Public date
2021-03-03
Experiment types
Non-coding RNA profiling by high throughput sequencing
Platforms
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Series type
Series
SubSeries
Not available
BioProject
PRJNA668373
Supplementary files
TAR: GSE159330_RAW.tar
Organism
Homo sapiens
Assay
bulk RNA-seq
Samples
34
Study design
Tumor vs unmatched normal
Specimen/source
Tissue
Scoring version
intent-aware-scoring-v15
Ranking batch
b69568dd1e4fe1b9ee2d880bf5495d748a7e4c5c11e4107f02528c3be0e76012
Ranking created
2026-06-05T20:20:27.088676Z
Warning version
intent-aware-warnings-v2

Current Intent Interpretation

Patient tissue tumor-vs-normal

Expectations

Organism
Homo sapiens
Assay
bulk RNA-seq
Specimen/source
patient tissue or biopsy
Controls
matched normal, adjacent normal, paired normal, healthy tissue control, or otherwise normal tissue control

Rules

Default filters
Human only; Bulk RNA-seq only; Tumor-normal only; Tissue or biopsy only; Hide biofluid/model systems
Warning rules
missing or unclear control group, unclear disease context, unclear tissue source, mixed sample types, model-system markers, secondary assay context, missing processed data, or small cohort size
Score caps
non-human datasets stay below the primary recommendation band, missing colorectal/colon/rectal/CRC context stays below the primary recommendation band, biofluid and model-system datasets cannot reach Recommended by default, microarray and secondary assays are capped unless explicitly enabled, or small cohorts are capped below high-confidence recommendations
Downgraded contexts
microarray unless explicitly enabled, biofluid-only datasets, cell-line datasets, organoid datasets, xenograft or PDX datasets, non-colorectal disease contexts, or treatment-only experiments

Study Classification

Tumor vs unmatched normal Tissue

Analysis Readiness

Review before analysis
94% DE readiness

Contrast completeness

25/25 pts

Both case and control groups are present in the proposed grouping.

Minimum group size

20/20 pts

Each contrast group has at least 2 samples.

Processed data availability

20/20 pts

Processed data is marked available in the GEO index.

Sample decision clarity

15/15 pts

All samples are assigned to a case or control group.

Blocking warnings

7/10 pts

Warnings are present, but none are critical blockers.

Metadata normalization

7/10 pts

Metadata quality is usable, but still deserves review.

Blockers

  • Secondary RNA assay context should be analyzed separately from ordinary bulk RNA-seq.

Next Steps

  • Review blockers and update sample grouping or dataset selection before analysis.

Analysis Preparation Checklist

5/6 ready

Group labels reviewed

Needs review

Siftome proposed case and control labels, but no reviewer confirmation is stored yet.

Open the sample grouping CSV and confirm group labels before analysis.

Minimum sample count met

Ready

Both groups meet the minimum of 2 samples.

Confirm whether the cohort is large enough for the intended statistical analysis.

Processed counts available

Ready

Processed data availability is marked true in the GEO index.

Verify that downloaded processed files contain usable count or expression identifiers.

Ambiguous samples handled

Ready

No review-needed or unassigned samples are present in the proposed grouping.

Still scan the grouping table for biology-specific ambiguity.

Exclusion decisions recorded

Ready

No hard-excluded samples were detected by the current rules.

Record any manual exclusions in the downstream analysis notes.

Source links preserved

Ready

The dataset and sample accessions can be linked back to GEO.

Keep GEO dataset and sample links with exported metadata.

Bioinformatician Review

Bioinformatician review required

Ask a bioinformatician to review grouping, count availability, exclusions, and design before DE.

  • Analysis readiness has blockers that must be resolved before DE.
  • Assay context may require expert handling before DESeq2-style analysis.

Why This Is Ranked Here

Patient tissue tumor-vs-normal
Not suitable Dataset does not meet the current suitability threshold.

Score Components

  • relevance 50% Organism normalized. Assay type normalized.
  • comparison suitability 0% Tumor and normal sample groups detected. No excluded sample type flags detected. Tumor/normal design boosted for colorectal tumor-vs-normal tissue triage. Patient tissue or biopsy specimens boosted for tissue comparison triage. Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking. Missing colorectal disease context downgraded for tumor-vs-normal tissue ranking.
  • metadata quality 70% Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. Group clarity: Rule-based grouping found both case and control samples. Disease clarity: Disease or condition metadata was not normalized. Tissue clarity: Tissue metadata was not normalized. Treatment clarity: No unclear treatment split detected in the sample metadata. Replicate clarity: No pooled sample or technical replicate flags detected. Data availability clarity: Dataset-level processed or raw data availability is explicit.
  • data availability 100% Processed data available. Raw data available.
  • overall 34% Weighted score: 30% relevance, 30% comparison suitability, 25% metadata quality, 15% data availability. Overall score capped because comparison suitability is weak for the selected search intent. Overall score capped because secondary RNA assays are not primary mRNA tissue RNA-seq. Overall score capped because colorectal/CRC disease context is not explicit.

Derived Classifications

  • Organism Homo sapiens Organism remains rule-derived: Homo sapiens.
  • Assay bulk RNA-seq Assay remains rule-derived: bulk RNA-seq.
  • Study design Tumor vs unmatched normal Study design remains rule-derived: Tumor vs unmatched normal.
  • Specimen/source Tissue Specimen/source remains rule-derived: Tissue.
  • Likely case group tumor sample 27 samples
  • Likely control group normal tissue 7 samples

Warnings

  • SECONDARY_ASSAY_CONTEXT warning Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.
  • DISEASE_LABEL_UNCLEAR warning Disease or condition label could not be normalized.
  • TISSUE_TYPE_MISSING warning Tissue or cell type could not be normalized.

Intent Interpretation

  • Active intent Patient tissue tumor-vs-normal Ranks human colorectal tissue or biopsy cohorts where tumor samples can be compared with normal controls.
  • Organism expectation Homo sapiens Dataset organism is interpreted as Homo sapiens.
  • Assay expectation bulk RNA-seq Dataset assay is interpreted as bulk RNA-seq.
  • Specimen assumption patient tissue or biopsy Derived specimen/source is Tissue.
  • Control-group assumption matched normal, adjacent normal, paired normal, healthy tissue control, or otherwise normal tissue control Derived study design is Tumor vs unmatched normal; likely groups are tumor sample vs normal tissue.
  • Score caps Applied when matching conditions are present non-human datasets stay below the primary recommendation band, missing colorectal/colon/rectal/CRC context stays below the primary recommendation band, biofluid and model-system datasets cannot reach Recommended by default, microarray and secondary assays are capped unless explicitly enabled, or small cohorts are capped below high-confidence recommendations
  • Warning rules 3 active warnings missing or unclear control group, unclear disease context, unclear tissue source, mixed sample types, model-system markers, secondary assay context, missing processed data, or small cohort size
  • Downgrade or exclusion reason Downgraded disease context: colorectal/GI relevance is unclear. Derived from current-intent ranking reasons and warnings.

Applied Review Decisions

No active review decisions affect this ranking.

Ranking Facts

  • Recommendation Not suitable Dataset does not meet the current suitability threshold.
  • Supporting fact Tumor vs unmatched normal · Tissue · suitability 0%. Contributed to match or upgrade evidence.
  • Supporting fact Prioritized assay: bulk RNA-seq is the active assay expectation. Contributed to match or upgrade evidence.
  • Supporting fact Downgraded disease context: colorectal/GI relevance is unclear. Contributed to match or upgrade evidence.
  • Supporting fact Processed data is available for downstream review. Contributed to match or upgrade evidence.
  • Supporting fact 3 warnings require review. Contributed to match or upgrade evidence.
  • Caution fact Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected. Contributed to downgrade or manual-review evidence.
  • Caution fact Disease or condition label could not be normalized. Contributed to downgrade or manual-review evidence.
  • Caution fact Tissue or cell type could not be normalized. Contributed to downgrade or manual-review evidence.
  • Caution fact Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking. Contributed to downgrade or manual-review evidence.
  • Caution fact Missing colorectal disease context downgraded for tumor-vs-normal tissue ranking. Contributed to downgrade or manual-review evidence.
  • Caution fact Missing or unclear metadata: Missing colorectal disease context downgraded for tumor-vs-normal tissue ranking. Contributed to downgrade or manual-review evidence.
  • Caution fact Missing or unclear metadata: Disease clarity: Disease or condition metadata was not normalized. Contributed to downgrade or manual-review evidence.
  • Caution fact Missing or unclear metadata: Tissue clarity: Tissue metadata was not normalized. Contributed to downgrade or manual-review evidence.
  • Caution fact Missing or unclear metadata: Treatment clarity: No unclear treatment split detected in the sample metadata. Contributed to downgrade or manual-review evidence.
  • Caution fact Overall score capped because comparison suitability is weak for the selected search intent. Contributed to downgrade or manual-review evidence.
  • Caution fact Overall score capped because secondary RNA assays are not primary mRNA tissue RNA-seq. Contributed to downgrade or manual-review evidence.
  • Caution fact Overall score capped because colorectal/CRC disease context is not explicit. Contributed to downgrade or manual-review evidence.
  • Caution fact Downgraded disease context: colorectal/GI relevance is unclear. Contributed to downgrade or manual-review evidence.
  • Caution fact Missing or unclear metadata: Downgraded disease context: colorectal/GI relevance is unclear. Contributed to downgrade or manual-review evidence.
  • Caution fact Comparison suitability score is below the Phase 1 recommended threshold. Contributed to downgrade or manual-review evidence.

Manual Corrections

0 active

Source Evidence

4 sources

GEO

Primary source

Original dataset metadata, sample metadata, source links, and GEO data availability flags.

Dataset accession
GSE159330
Sample records
34 GSM samples
  • GEO has priority for original metadata under the Phase 3J source rules.
  • Processed data: available.
  • Raw data: available.
  • No external source conflict is present in the current runtime data.

recount3

Not imported

Planned trusted source for processed count availability.

GEO accession
GSE159330
  • No recount3 project identifier has been imported for this dataset.
  • Once imported, recount3 has priority for processed count availability.
  • The recount3 source filter excludes this dataset until that linkage exists.
No recount3 sync data available.

Expression Atlas

Not imported

Planned source for curated expression experiment links.

GEO accession
GSE159330
  • No Expression Atlas experiment identifier has been imported for this dataset.
  • Once imported, Expression Atlas has priority for curated expression experiment links.
  • The Expression Atlas source filter excludes this dataset until that linkage exists.
No Expression Atlas sync data available.

PubMed

Unavailable

Publication context when PubMed identifiers are already known.

GEO accession
GSE159330
  • No PubMed identifier is present in the current runtime metadata.
  • No live PubMed search is performed from the dataset detail page.
No publication identifier imported.

Dataset Feedback

0 stored

Original GEO Metadata

dataset_accession: GSE159330
dataset_title: Expression profiling by small RNA-seq for identifying miRNAs associated with pathological classifications in thyroid cancer.
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2020-10-09
last_update_date: 2021-03-03
organization_name: Korea Research Institutue of Bioscience & Biotechnology
department: Personalized Genomic Medicine Research Center
public_date: 2021-03-03
experiment_types: Non-coding RNA profiling by high throughput sequencing
platforms: GPL18573 Illumina NextSeq 500 (Homo sapiens)
sub_series: Not available
bioproject: PRJNA668373
supplementary_files: TAR: GSE159330_RAW.tar
series_type: Series

Why It Matched

  • Tumor vs unmatched normal · Tissue · suitability 0%.
  • Prioritized assay: bulk RNA-seq is the active assay expectation.
  • Downgraded disease context: colorectal/GI relevance is unclear.
  • Processed data is available for downstream review.
  • 3 warnings require review.

Why It May Not Be Suitable

  • Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.
  • Disease or condition label could not be normalized.
  • Tissue or cell type could not be normalized.
  • Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking.
  • Missing colorectal disease context downgraded for tumor-vs-normal tissue ranking.
  • Missing or unclear metadata: Missing colorectal disease context downgraded for tumor-vs-normal tissue ranking.
  • Missing or unclear metadata: Disease clarity: Disease or condition metadata was not normalized.
  • Missing or unclear metadata: Tissue clarity: Tissue metadata was not normalized.
  • Missing or unclear metadata: Treatment clarity: No unclear treatment split detected in the sample metadata.
  • Overall score capped because comparison suitability is weak for the selected search intent.
  • Overall score capped because secondary RNA assays are not primary mRNA tissue RNA-seq.
  • Overall score capped because colorectal/CRC disease context is not explicit.
  • Downgraded disease context: colorectal/GI relevance is unclear.
  • Missing or unclear metadata: Downgraded disease context: colorectal/GI relevance is unclear.
  • Comparison suitability score is below the Phase 1 recommended threshold.

Warnings

  • warning SECONDARY_ASSAY_CONTEXT Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.
  • warning DISEASE_LABEL_UNCLEAR Disease or condition label could not be normalized.
  • warning TISSUE_TYPE_MISSING Tissue or cell type could not be normalized.

Normalized Fields

36 fields
Field Value Source Origin Confidence Evidence Reason
assay_type bulk RNA-seq dataset GSE159330 Runtime Siftome inference GEO:dataset:GSE159330:85de0721ffc1e8f14d310e69328f9efe56019ead3d63edd8a06e2be246e261f8 high confidence bulk rna-seq dataset_accession: GSE159330 dataset_title: Expression profiling by small RNA-seq for identifying miRNAs associated with pathological classifications in thyroid cancer. organism... keyword match keyword match: bulk rna-seq
organism Homo sapiens dataset GSE159330 Runtime Siftome inference GEO:dataset:GSE159330:85de0721ffc1e8f14d310e69328f9efe56019ead3d63edd8a06e2be246e261f8 high confidence homo sapiens dataset_accession: GSE159330 dataset_title: Expression profiling by small RNA-seq for identifying miRNAs associated with pathological classifications in thyroid cancer. organism... keyword match keyword match: homo sapiens
sample_type tumor sample sample GSM4826760 Runtime Siftome inference GEO:sample:GSM4826760:6c8e1b03975efc65236169ded5e2a44104d3c5b3ac4094463b76941374d37471 low confidence tumor sample_accession: GSM4826760 sample_title: S02T_miRNA-seq source_name: Thyroid tumor tissue characteristics: pathological type: EFV, invasive; age: 46; gender: M S02T_miRNA-seq controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM4826761 Runtime Siftome inference GEO:sample:GSM4826761:659fe0384f262abe1778f055d1bf21bf08b68aa21cec529caa745585b37ca7aa low confidence tumor sample_accession: GSM4826761 sample_title: S03T_miRNA-seq source_name: Thyroid tumor tissue characteristics: pathological type: Tall cell; age: 36; gender: M S03T_miRNA-seq controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM4826762 Runtime Siftome inference GEO:sample:GSM4826762:1c319803ba6afc55ae724d4ee2934a0ca9d4f8134e13a2d3c5e0b5b8c8fab32c low confidence tumor sample_accession: GSM4826762 sample_title: S04T_miRNA-seq source_name: Thyroid tumor tissue characteristics: pathological type: Classic; age: 40; gender: F S04T_miRNA-seq controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM4826763 Runtime Siftome inference GEO:sample:GSM4826763:209ac5b6181a9feb50d4c3deb6e005bd7e6c73f9dd7a1a03b59c5954b0fc3d91 low confidence tumor sample_accession: GSM4826763 sample_title: S06T_miRNA-seq source_name: Thyroid tumor tissue characteristics: pathological type: Classic; age: 36; gender: F S06T_miRNA-seq controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM4826764 Runtime Siftome inference GEO:sample:GSM4826764:28d4a9853139697df1b3838fd496fb35368e57e2334453c51cf6e47b982255ae low confidence tumor sample_accession: GSM4826764 sample_title: S07T_miRNA-seq source_name: Thyroid tumor tissue characteristics: pathological type: Classic; age: 31; gender: F S07T_miRNA-seq controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM4826765 Runtime Siftome inference GEO:sample:GSM4826765:4ef5bca53ef60fca36688706860388d0cb574832d38ccea773de80a8a9db757a low confidence tumor sample_accession: GSM4826765 sample_title: S09T_miRNA-seq source_name: Thyroid tumor tissue characteristics: pathological type: EFV, invasive; age: 55; gender: F S09T_miRNA-seq controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM4826766 Runtime Siftome inference GEO:sample:GSM4826766:5413a5ee45e07524515688fcf71730643724b04753419b4c38941bce94dbe635 low confidence tumor sample_accession: GSM4826766 sample_title: S10T_miRNA-seq source_name: Thyroid tumor tissue characteristics: pathological type: NIFTP; age: 51; gender: M S10T_miRNA-seq controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM4826767 Runtime Siftome inference GEO:sample:GSM4826767:5cb9f9c46de05e9ef5e17551af6083968418643d567c1d0cd6ba209c44f88bd9 low confidence tumor sample_accession: GSM4826767 sample_title: S11T_miRNA-seq source_name: Thyroid tumor tissue characteristics: pathological type: Tall cell; age: 52; gender: F S11T_miRNA-seq controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM4826768 Runtime Siftome inference GEO:sample:GSM4826768:2f6d60a15b9198a67a6f5cd818ced258b2d26706d8e5a9ef2b3227ce111998e6 low confidence tumor sample_accession: GSM4826768 sample_title: S12T_miRNA-seq source_name: Thyroid tumor tissue characteristics: pathological type: Classic; age: 41; gender: F S12T_miRNA-seq controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM4826769 Runtime Siftome inference GEO:sample:GSM4826769:ec51f3ac47ddcc287ca4e0159de52d9be1d76ba36518f11675abbaaac8cdbfc6 low confidence tumor sample_accession: GSM4826769 sample_title: S13T_miRNA-seq source_name: Thyroid tumor tissue characteristics: pathological type: Tall cell; age: 26; gender: F S13T_miRNA-seq controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM4826770 Runtime Siftome inference GEO:sample:GSM4826770:9743911059b69aa913364fc7b327a9bfd3030dbd1c0b7f050eaa35c107ac1271 low confidence tumor sample_accession: GSM4826770 sample_title: S14T_miRNA-seq source_name: Thyroid tumor tissue characteristics: pathological type: Tall cell; age: 57; gender: F S14T_miRNA-seq controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM4826771 Runtime Siftome inference GEO:sample:GSM4826771:af6f585976ef8adab62d3d07ffcda84dbbe53a449243c705ca91cff8d5786ac4 low confidence tumor sample_accession: GSM4826771 sample_title: S15T_miRNA-seq source_name: Thyroid tumor tissue characteristics: pathological type: Classic; age: 31; gender: M S15T_miRNA-seq controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM4826772 Runtime Siftome inference GEO:sample:GSM4826772:895093666990859c0d99d9a196d134f7d965688398e5615bb126de85f0b96339 low confidence tumor sample_accession: GSM4826772 sample_title: S19T_miRNA-seq source_name: Thyroid tumor tissue characteristics: pathological type: Classic; age: 37; gender: M S19T_miRNA-seq controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM4826773 Runtime Siftome inference GEO:sample:GSM4826773:3fdd0fe49f97a2db081126e7e539f5c3ba687f93e6424cf88bf48afb31fe9282 low confidence tumor sample_accession: GSM4826773 sample_title: S20T_miRNA-seq source_name: Thyroid tumor tissue characteristics: pathological type: Tall cell; age: 47; gender: F S20T_miRNA-seq controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM4826774 Runtime Siftome inference GEO:sample:GSM4826774:764ffcf664259ef8a4e19a4e612a3f9a8005fc29aa855aad23ddc8de2ac4c1bb low confidence tumor sample_accession: GSM4826774 sample_title: S22T_miRNA-seq source_name: Thyroid tumor tissue characteristics: pathological type: Classic; age: 38; gender: F S22T_miRNA-seq controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM4826775 Runtime Siftome inference GEO:sample:GSM4826775:3835f7895f302166097795d505fc5b0437a262eb22ed0501a0909810fbe72204 low confidence tumor sample_accession: GSM4826775 sample_title: S23T_miRNA-seq source_name: Thyroid tumor tissue characteristics: pathological type: NIFTP; age: 31; gender: M S23T_miRNA-seq controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM4826776 Runtime Siftome inference GEO:sample:GSM4826776:35970c0da218b970e3f2146784adde1b6c9a7fa065ee07569f2ee50d5a79bd89 low confidence tumor sample_accession: GSM4826776 sample_title: S25T_miRNA-seq source_name: Thyroid tumor tissue characteristics: pathological type: Tall cell; age: 68; gender: F S25T_miRNA-seq controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM4826777 Runtime Siftome inference GEO:sample:GSM4826777:cc8c811da75cd80c58abee7c326f6f11c9f2787bcb7c017352d55fd5932a44d6 low confidence tumor sample_accession: GSM4826777 sample_title: S27T_miRNA-seq source_name: Thyroid tumor tissue characteristics: pathological type: NIFTP; age: 51; gender: F S27T_miRNA-seq controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM4826778 Runtime Siftome inference GEO:sample:GSM4826778:bec0091901da44143d29f6e74eccdba74124829a55f6b7f760951d15138727a4 low confidence tumor sample_accession: GSM4826778 sample_title: S28T_miRNA-seq source_name: Thyroid tumor tissue characteristics: pathological type: EFV, invasive; age: 62; gender: F S28T_miRNA-seq controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM4826779 Runtime Siftome inference GEO:sample:GSM4826779:2d847ab044ebd63f11fcbf18dd5515a8a57c4f54f261e79d157f742d800f85f1 low confidence tumor sample_accession: GSM4826779 sample_title: S32T_miRNA-seq source_name: Thyroid tumor tissue characteristics: pathological type: Classic; age: 52; gender: F S32T_miRNA-seq controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM4826780 Runtime Siftome inference GEO:sample:GSM4826780:9b62b060b1906afdfcbcd0fc9c13b825b8d2773d641c31b811cda4c7ea3df4f6 low confidence tumor sample_accession: GSM4826780 sample_title: S34T_miRNA-seq source_name: Thyroid tumor tissue characteristics: pathological type: NIFTP; age: 44; gender: M S34T_miRNA-seq controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM4826781 Runtime Siftome inference GEO:sample:GSM4826781:93a7a157bb1897fe85b89365a5f7660056f960d1635adfb5d0e7776cbaf749f6 low confidence tumor sample_accession: GSM4826781 sample_title: S35T_miRNA-seq source_name: Thyroid tumor tissue characteristics: pathological type: Classic; age: 28; gender: M S35T_miRNA-seq controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM4826782 Runtime Siftome inference GEO:sample:GSM4826782:a7dee9816140c02332cf6c6b2b7ee9abd15a1498d1d4496ae2341cac33e7c725 low confidence tumor sample_accession: GSM4826782 sample_title: S37T_miRNA-seq source_name: Thyroid tumor tissue characteristics: pathological type: Classic; age: 32; gender: F S37T_miRNA-seq controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM4826783 Runtime Siftome inference GEO:sample:GSM4826783:8b64519c90a96d100315caac8189248b943bebe428618471dbf1451aec8789c4 low confidence tumor sample_accession: GSM4826783 sample_title: S38T_miRNA-seq source_name: Thyroid tumor tissue characteristics: pathological type: Tall cell; age: 70; gender: M S38T_miRNA-seq controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM4826784 Runtime Siftome inference GEO:sample:GSM4826784:239d5ae9400e27f9eb3035665f25bb44bb11e5c2e9177281a9ddb7c2f443d9ce low confidence tumor sample_accession: GSM4826784 sample_title: S39T_miRNA-seq source_name: Thyroid tumor tissue characteristics: pathological type: NIFTP; age: 60; gender: F S39T_miRNA-seq controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM4826785 Runtime Siftome inference GEO:sample:GSM4826785:729ba663b5a9127fdfdae7f9ccd82153f8439961a8dbf9c729f250951b6b6f03 low confidence tumor sample_accession: GSM4826785 sample_title: S40T_miRNA-seq source_name: Thyroid tumor tissue characteristics: pathological type: NIFTP; age: 47; gender: F S40T_miRNA-seq controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM4826786 Runtime Siftome inference GEO:sample:GSM4826786:c9a9dff13c74a7b075cc0e1e909c885f2a5d18bffc918bccc782443b14824c86 low confidence tumor sample_accession: GSM4826786 sample_title: S41T_miRNA-seq source_name: Thyroid tumor tissue characteristics: pathological type: Classic; age: 44; gender: F S41T_miRNA-seq controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM4826787 Runtime Siftome inference GEO:sample:GSM4826787:46681bf2904aebf8a6a2e477aafa22316c83e1c1c04a37c01a56c1ef7f9ebea4 medium confidence non-tumor sample_accession: GSM4826787 sample_title: S02N_miRNA-seq source_name: Normal thyroid tissue characteristics: pathological type: non-tumor S02N_miRNA-seq controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type normal tissue sample GSM4826788 Runtime Siftome inference GEO:sample:GSM4826788:ce9772984c2b670606687940a64f5eb42e925508335332ec394a73286675df16 medium confidence non-tumor sample_accession: GSM4826788 sample_title: S09N_miRNA-seq source_name: Normal thyroid tissue characteristics: pathological type: non-tumor S09N_miRNA-seq controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type normal tissue sample GSM4826789 Runtime Siftome inference GEO:sample:GSM4826789:a33a2ea6e51181b7d9bfe6b9d8fbf0fbe1d55b3c3828959d224724222bfa016a medium confidence non-tumor sample_accession: GSM4826789 sample_title: S23N_miRNA-seq source_name: Normal thyroid tissue characteristics: pathological type: non-tumor S23N_miRNA-seq controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type normal tissue sample GSM4826790 Runtime Siftome inference GEO:sample:GSM4826790:15c8dcdbde4486ebb2162b535bd5cb0c3e7ce465593f6a207eed23062cbdb292 medium confidence non-tumor sample_accession: GSM4826790 sample_title: S27N_miRNA-seq source_name: Normal thyroid tissue characteristics: pathological type: non-tumor S27N_miRNA-seq controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type normal tissue sample GSM4826791 Runtime Siftome inference GEO:sample:GSM4826791:3f949e2f7241da1ce64954f670a82904e63c0ac7d8382c8581bd03d7b8e89210 medium confidence non-tumor sample_accession: GSM4826791 sample_title: S34N_miRNA-seq source_name: Normal thyroid tissue characteristics: pathological type: non-tumor S34N_miRNA-seq controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type normal tissue sample GSM4826792 Runtime Siftome inference GEO:sample:GSM4826792:fe1a9b30f0ebef0a7806120673c7b8f3e90879f71ef764fec95d5939ad636304 medium confidence non-tumor sample_accession: GSM4826792 sample_title: S39N_miRNA-seq source_name: Normal thyroid tissue characteristics: pathological type: non-tumor S39N_miRNA-seq controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type normal tissue sample GSM4826793 Runtime Siftome inference GEO:sample:GSM4826793:2774b491de06121273e924de772620b8c43b974ccef22862f775816e8c7e3472 medium confidence non-tumor sample_accession: GSM4826793 sample_title: S40N_miRNA-seq source_name: Normal thyroid tissue characteristics: pathological type: non-tumor S40N_miRNA-seq controlled vocabulary controlled vocabulary sample type match: non-tumor

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

27
  • GSM4826760 S02T_miRNA-seq tumor sample Case marker detected. Thyroid tumor tissue pathological type: EFV, invasive; age: 46; gender: M
  • GSM4826761 S03T_miRNA-seq tumor sample Case marker detected. Thyroid tumor tissue pathological type: Tall cell; age: 36; gender: M
  • GSM4826762 S04T_miRNA-seq tumor sample Case marker detected. Thyroid tumor tissue pathological type: Classic; age: 40; gender: F
  • GSM4826763 S06T_miRNA-seq tumor sample Case marker detected. Thyroid tumor tissue pathological type: Classic; age: 36; gender: F
  • GSM4826764 S07T_miRNA-seq tumor sample Case marker detected. Thyroid tumor tissue pathological type: Classic; age: 31; gender: F
  • GSM4826765 S09T_miRNA-seq tumor sample Case marker detected. Thyroid tumor tissue pathological type: EFV, invasive; age: 55; gender: F
  • GSM4826766 S10T_miRNA-seq tumor sample Case marker detected. Thyroid tumor tissue pathological type: NIFTP; age: 51; gender: M
  • GSM4826767 S11T_miRNA-seq tumor sample Case marker detected. Thyroid tumor tissue pathological type: Tall cell; age: 52; gender: F
  • GSM4826768 S12T_miRNA-seq tumor sample Case marker detected. Thyroid tumor tissue pathological type: Classic; age: 41; gender: F
  • GSM4826769 S13T_miRNA-seq tumor sample Case marker detected. Thyroid tumor tissue pathological type: Tall cell; age: 26; gender: F
  • GSM4826770 S14T_miRNA-seq tumor sample Case marker detected. Thyroid tumor tissue pathological type: Tall cell; age: 57; gender: F
  • GSM4826771 S15T_miRNA-seq tumor sample Case marker detected. Thyroid tumor tissue pathological type: Classic; age: 31; gender: M
  • GSM4826772 S19T_miRNA-seq tumor sample Case marker detected. Thyroid tumor tissue pathological type: Classic; age: 37; gender: M
  • GSM4826773 S20T_miRNA-seq tumor sample Case marker detected. Thyroid tumor tissue pathological type: Tall cell; age: 47; gender: F
  • GSM4826774 S22T_miRNA-seq tumor sample Case marker detected. Thyroid tumor tissue pathological type: Classic; age: 38; gender: F
  • GSM4826775 S23T_miRNA-seq tumor sample Case marker detected. Thyroid tumor tissue pathological type: NIFTP; age: 31; gender: M
  • GSM4826776 S25T_miRNA-seq tumor sample Case marker detected. Thyroid tumor tissue pathological type: Tall cell; age: 68; gender: F
  • GSM4826777 S27T_miRNA-seq tumor sample Case marker detected. Thyroid tumor tissue pathological type: NIFTP; age: 51; gender: F
  • GSM4826778 S28T_miRNA-seq tumor sample Case marker detected. Thyroid tumor tissue pathological type: EFV, invasive; age: 62; gender: F
  • GSM4826779 S32T_miRNA-seq tumor sample Case marker detected. Thyroid tumor tissue pathological type: Classic; age: 52; gender: F
  • GSM4826780 S34T_miRNA-seq tumor sample Case marker detected. Thyroid tumor tissue pathological type: NIFTP; age: 44; gender: M
  • GSM4826781 S35T_miRNA-seq tumor sample Case marker detected. Thyroid tumor tissue pathological type: Classic; age: 28; gender: M
  • GSM4826782 S37T_miRNA-seq tumor sample Case marker detected. Thyroid tumor tissue pathological type: Classic; age: 32; gender: F
  • GSM4826783 S38T_miRNA-seq tumor sample Case marker detected. Thyroid tumor tissue pathological type: Tall cell; age: 70; gender: M
  • GSM4826784 S39T_miRNA-seq tumor sample Case marker detected. Thyroid tumor tissue pathological type: NIFTP; age: 60; gender: F
  • GSM4826785 S40T_miRNA-seq tumor sample Case marker detected. Thyroid tumor tissue pathological type: NIFTP; age: 47; gender: F
  • GSM4826786 S41T_miRNA-seq tumor sample Case marker detected. Thyroid tumor tissue pathological type: Classic; age: 44; gender: F

Possible control samples

Samples currently treated as controls or baseline.

7
  • GSM4826787 S02N_miRNA-seq normal tissue Control marker detected. Normal thyroid tissue pathological type: non-tumor
  • GSM4826788 S09N_miRNA-seq normal tissue Control marker detected. Normal thyroid tissue pathological type: non-tumor
  • GSM4826789 S23N_miRNA-seq normal tissue Control marker detected. Normal thyroid tissue pathological type: non-tumor
  • GSM4826790 S27N_miRNA-seq normal tissue Control marker detected. Normal thyroid tissue pathological type: non-tumor
  • GSM4826791 S34N_miRNA-seq normal tissue Control marker detected. Normal thyroid tissue pathological type: non-tumor
  • GSM4826792 S39N_miRNA-seq normal tissue Control marker detected. Normal thyroid tissue pathological type: non-tumor
  • GSM4826793 S40N_miRNA-seq normal tissue Control marker detected. Normal thyroid tissue pathological type: non-tumor

Unassigned samples

Samples with no explicit case or control marker.

0

No samples

Excluded samples

Samples excluded from grouping by hard exclusion rules.

0

No samples

Ambiguous samples

Samples that need manual review before trusting grouping.

0

No samples

Metadata Quality Components

Persisted metadata quality

70 pts
Clarity
70%
Weight
100 pts

Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. Group clarity: Rule-based grouping found both case and control samples. Disease clarity: Disease or condition metadata was not normalized. Tissue clarity: Tissue metadata was not normalized. Treatment clarity: No unclear treatment split detected in the sample metadata. Replicate clarity: No pooled sample or technical replicate flags detected. Data availability clarity: Dataset-level processed or raw data availability is explicit.

Detected Sample Groups

tumor sample

27 samples
  • GSM4826760 S02T_miRNA-seq Thyroid tumor tissue pathological type: EFV, invasive; age: 46; gender: M
  • GSM4826761 S03T_miRNA-seq Thyroid tumor tissue pathological type: Tall cell; age: 36; gender: M
  • GSM4826762 S04T_miRNA-seq Thyroid tumor tissue pathological type: Classic; age: 40; gender: F
  • GSM4826763 S06T_miRNA-seq Thyroid tumor tissue pathological type: Classic; age: 36; gender: F
  • GSM4826764 S07T_miRNA-seq Thyroid tumor tissue pathological type: Classic; age: 31; gender: F
  • GSM4826765 S09T_miRNA-seq Thyroid tumor tissue pathological type: EFV, invasive; age: 55; gender: F
  • GSM4826766 S10T_miRNA-seq Thyroid tumor tissue pathological type: NIFTP; age: 51; gender: M
  • GSM4826767 S11T_miRNA-seq Thyroid tumor tissue pathological type: Tall cell; age: 52; gender: F
  • GSM4826768 S12T_miRNA-seq Thyroid tumor tissue pathological type: Classic; age: 41; gender: F
  • GSM4826769 S13T_miRNA-seq Thyroid tumor tissue pathological type: Tall cell; age: 26; gender: F
  • GSM4826770 S14T_miRNA-seq Thyroid tumor tissue pathological type: Tall cell; age: 57; gender: F
  • GSM4826771 S15T_miRNA-seq Thyroid tumor tissue pathological type: Classic; age: 31; gender: M
  • GSM4826772 S19T_miRNA-seq Thyroid tumor tissue pathological type: Classic; age: 37; gender: M
  • GSM4826773 S20T_miRNA-seq Thyroid tumor tissue pathological type: Tall cell; age: 47; gender: F
  • GSM4826774 S22T_miRNA-seq Thyroid tumor tissue pathological type: Classic; age: 38; gender: F
  • GSM4826775 S23T_miRNA-seq Thyroid tumor tissue pathological type: NIFTP; age: 31; gender: M
  • GSM4826776 S25T_miRNA-seq Thyroid tumor tissue pathological type: Tall cell; age: 68; gender: F
  • GSM4826777 S27T_miRNA-seq Thyroid tumor tissue pathological type: NIFTP; age: 51; gender: F
  • GSM4826778 S28T_miRNA-seq Thyroid tumor tissue pathological type: EFV, invasive; age: 62; gender: F
  • GSM4826779 S32T_miRNA-seq Thyroid tumor tissue pathological type: Classic; age: 52; gender: F
  • GSM4826780 S34T_miRNA-seq Thyroid tumor tissue pathological type: NIFTP; age: 44; gender: M
  • GSM4826781 S35T_miRNA-seq Thyroid tumor tissue pathological type: Classic; age: 28; gender: M
  • GSM4826782 S37T_miRNA-seq Thyroid tumor tissue pathological type: Classic; age: 32; gender: F
  • GSM4826783 S38T_miRNA-seq Thyroid tumor tissue pathological type: Tall cell; age: 70; gender: M
  • GSM4826784 S39T_miRNA-seq Thyroid tumor tissue pathological type: NIFTP; age: 60; gender: F
  • GSM4826785 S40T_miRNA-seq Thyroid tumor tissue pathological type: NIFTP; age: 47; gender: F
  • GSM4826786 S41T_miRNA-seq Thyroid tumor tissue pathological type: Classic; age: 44; gender: F

normal tissue

7 samples
  • GSM4826787 S02N_miRNA-seq Normal thyroid tissue pathological type: non-tumor
  • GSM4826788 S09N_miRNA-seq Normal thyroid tissue pathological type: non-tumor
  • GSM4826789 S23N_miRNA-seq Normal thyroid tissue pathological type: non-tumor
  • GSM4826790 S27N_miRNA-seq Normal thyroid tissue pathological type: non-tumor
  • GSM4826791 S34N_miRNA-seq Normal thyroid tissue pathological type: non-tumor
  • GSM4826792 S39N_miRNA-seq Normal thyroid tissue pathological type: non-tumor
  • GSM4826793 S40N_miRNA-seq Normal thyroid tissue pathological type: non-tumor

Score Breakdown

50%

relevance

  • Organism normalized.
  • Assay type normalized.
0%

comparison suitability

  • Tumor and normal sample groups detected.
  • No excluded sample type flags detected.
  • Tumor/normal design boosted for colorectal tumor-vs-normal tissue triage.
  • Patient tissue or biopsy specimens boosted for tissue comparison triage.
  • Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking.
  • Missing colorectal disease context downgraded for tumor-vs-normal tissue ranking.
70%

metadata quality

  • Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
  • Group clarity: Rule-based grouping found both case and control samples.
  • Disease clarity: Disease or condition metadata was not normalized.
  • Tissue clarity: Tissue metadata was not normalized.
  • Treatment clarity: No unclear treatment split detected in the sample metadata.
  • Replicate clarity: No pooled sample or technical replicate flags detected.
  • Data availability clarity: Dataset-level processed or raw data availability is explicit.
100%

data availability

  • Processed data available.
  • Raw data available.
34%

overall

  • Weighted score: 30% relevance, 30% comparison suitability, 25% metadata quality, 15% data availability.
  • Overall score capped because comparison suitability is weak for the selected search intent.
  • Overall score capped because secondary RNA assays are not primary mRNA tissue RNA-seq.
  • Overall score capped because colorectal/CRC disease context is not explicit.

Sample Links

34 samples

Review Audit Trail

0 decisions

No review decisions have been stored for this dataset.