id stringlengths 12 40 | prompt stringlengths 1.11k 1.94k | ground_truth_response null | label stringclasses 3
values | pert_type stringclasses 2
values | model_output stringlengths 486 17.4k |
|---|---|---|---|---|---|
B cells_Alogliptin_ARHGEF19 | You are an expert biologist. Your goal is to determine: Is the expression of ARHGEF19 up, down, or unchanged after chemical perturbation Alogliptin in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
... | null | unchanged | chemical | <thinking>Alogliptin inhibits DPP4, which normally activates TGFB1; however, since TGFB1 is already at medium basal levels, the reduction in DPP4 activity results in only a modest decrease in TGFB1 signaling, insufficient to significantly alter downstream TP53 activation. TP53, which is basally low, remains largely uni... |
B cells_Alogliptin_COL4A3 | You are an expert biologist. Your goal is to determine: Is the expression of COL4A3 up, down, or unchanged after chemical perturbation Alogliptin in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
#... | null | unchanged | chemical | <thinking>Alogliptin inhibits DPP4, which reduces activation of TGFB1, leading to diminished stimulation of TP53; however, TP53's activation of COL4A3 is already constrained by the low basal expression level of COL4A3, which serves as a molecular floor, limiting the magnitude of any transcriptional response. Given that... |
B cells_Alogliptin_DDB1 | You are an expert biologist. Your goal is to determine: Is the expression of DDB1 up, down, or unchanged after chemical perturbation Alogliptin in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
## ... | null | unchanged | chemical | <thinking>Alogliptin inhibits DPP4, which reduces activation of TGFB1, leading to diminished stimulation of TP53; however, TP53's activation of DDB1 is minimal due to the low basal expression of DDB1 and the weak transcriptional responsiveness of this gene to TP53 signaling, resulting in no significant change in DDB1 e... |
B cells_Alogliptin_DTWD1 | You are an expert biologist. Your goal is to determine: Is the expression of DTWD1 up, down, or unchanged after chemical perturbation Alogliptin in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
##... | null | unchanged | chemical | <thinking>Alogliptin inhibits DPP4, which disrupts the activation of TGFB1, a medium-expressed gene that normally activates TP53, a low-expressed gene that in turn regulates DTWD1, a gene with low basal expression. Despite this linear pathway, DTWD1 expression remains unchanged because the basal level of DTWD1 is alrea... |
B cells_Alogliptin_FES | You are an expert biologist. Your goal is to determine: Is the expression of FES up, down, or unchanged after chemical perturbation Alogliptin in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
## T... | null | unchanged | chemical | <thinking>Alogliptin inhibits DPP4, which reduces activation of ITGB1, leading to diminished stimulation of RAC1; however, RAC1 operates at medium basal levels and its downstream activation of FES is constrained by the low basal expression of FES, which serves as a molecular floor limiting dynamic response. Given that ... |
B cells_Alogliptin_GAB2 | You are an expert biologist. Your goal is to determine: Is the expression of GAB2 up, down, or unchanged after chemical perturbation Alogliptin in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
## ... | null | unchanged | chemical | <thinking>Alogliptin inhibits DPP4, which reduces activation of ITGB1, leading to diminished stimulation of RHOA; however, RHOA's activation of GAB2 is not significantly altered because GAB2 exhibits low basal expression and is already operating near a physiological floor, such that even moderate reductions in upstream... |
B cells_Alogliptin_GSN | You are an expert biologist. Your goal is to determine: Is the expression of GSN up, down, or unchanged after chemical perturbation Alogliptin in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
## T... | null | unchanged | chemical | <thinking>Alogliptin inhibits DPP4, which reduces activation of TGFB1, leading to diminished stimulation of TP53; however, TP53's activation of GSN is already constrained by the low basal expression of GSN, which serves as a molecular floor, limiting the magnitude of any transcriptional response. Given that the basal l... |
B cells_Alogliptin_IGFBP7 | You are an expert biologist. Your goal is to determine: Is the expression of IGFBP7 up, down, or unchanged after chemical perturbation Alogliptin in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
#... | null | unchanged | chemical | <thinking>Alogliptin inhibits DPP4, which normally activates TGFB1; however, since TGFB1 is already at medium basal levels, the reduction in DPP4 activity results in only a modest decrease in TGFB1 signaling, insufficient to significantly elevate TP53, which remains at low basal levels. Given that TP53 is a key activat... |
B cells_Alogliptin_LIMK2 | You are an expert biologist. Your goal is to determine: Is the expression of LIMK2 up, down, or unchanged after chemical perturbation Alogliptin in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
##... | null | unchanged | chemical | <thinking>Alogliptin inhibits DPP4, which disrupts the activation of TGFB1, a medium-expressed gene that normally activates TP53, a low-expressed gene that in turn regulates LIMK2. Given that LIMK2 is already at low basal expression, the downstream suppression of TP53 by reduced TGFB1 signaling results in minimal chang... |
B cells_Alogliptin_MGRN1 | You are an expert biologist. Your goal is to determine: Is the expression of MGRN1 up, down, or unchanged after chemical perturbation Alogliptin in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
##... | null | unchanged | chemical | <thinking>Alogliptin inhibits DPP4, which disrupts the activation of TGFB1, a medium-expressed gene that normally activates TP53, a low-expressed gene that in turn regulates MGRN1, a gene with low basal expression. Given that the basal level of MGRN1 is already low, and the pathway from DPP4 to MGRN1 operates through a... |
B cells_Alogliptin_NUAK1 | You are an expert biologist. Your goal is to determine: Is the expression of NUAK1 up, down, or unchanged after chemical perturbation Alogliptin in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
##... | null | unchanged | chemical | <thinking>Alogliptin inhibits DPP4, which normally activates TGFB1; however, since TGFB1 is already at medium basal levels, the reduction in DPP4 activity results in only a modest decrease in TGFB1 signaling, insufficient to significantly alter downstream TP53 activation. TP53, which is basally low, remains largely ina... |
B cells_Alogliptin_PTMA | You are an expert biologist. Your goal is to determine: Is the expression of PTMA up, down, or unchanged after chemical perturbation Alogliptin in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
## ... | null | down | chemical | <thinking>Alogliptin inhibits DPP4, disrupting its normal function in the regulatory network, which leads to reduced activation of TGFB1, a key upstream activator of PTMA. However, given that DPP4 is a low-basal-expressing component and its inhibition results in diminished TGFB1 signaling, the downstream activation of ... |
B cells_Alogliptin_SMPD3 | You are an expert biologist. Your goal is to determine: Is the expression of SMPD3 up, down, or unchanged after chemical perturbation Alogliptin in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
##... | null | unchanged | chemical | <thinking>Alogliptin inhibits DPP4, which reduces activation of TGFB1, leading to diminished stimulation of TP53; however, TP53's activation of SMPD3 is not significantly altered because SMPD3 maintains low basal expression and is subject to minimal transcriptional flux under these conditions, such that even reduced TP... |
B cells_Alvocidib_ACP2 | You are an expert biologist. Your goal is to determine: Is the expression of ACP2 up, down, or unchanged after chemical perturbation Alvocidib in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
## T... | null | unchanged | chemical | <thinking>Alvocidib inhibits CDK7 and CDK9, leading to reduced activation of TP53 and RB1, respectively; however, TP53 and RB1 both contribute to the activation of YY1, and YY1 is a key regulator of ACP2. Despite the inhibition of upstream kinases, the basal expression of ACP2 is low, and the pathway from CDK7/CDK9 to ... |
B cells_Alvocidib_ADAMTS10 | You are an expert biologist. Your goal is to determine: Is the expression of ADAMTS10 up, down, or unchanged after chemical perturbation Alvocidib in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
... | null | unchanged | chemical | <thinking>Alvocidib inhibits CDK1, CDK7, and GSK3A, leading to reduced activation of TP53 and E2F4, respectively; however, TP53 and E2F4 both act as transcriptional regulators of ADAMTS10, and their basal expression levels are low, resulting in minimal baseline activation of ADAMTS10. Despite the inhibition of upstream... |
B cells_Alvocidib_ADAMTSL4-AS1 | You are an expert biologist. Your goal is to determine: Is the expression of ADAMTSL4-AS1 up, down, or unchanged after chemical perturbation Alvocidib in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gen... | null | unchanged | chemical | <thinking>Alvocidib inhibits CDK7 and GAK, leading to reduced activation of AR through both CDK7-mediated activation and GAK-mediated activation, while simultaneously relieving inhibition of AR via GSK3B suppression; however, due to the low basal expression of AR and the presence of redundant regulatory inputs, AR acti... |
B cells_Alvocidib_AIRE | You are an expert biologist. Your goal is to determine: Is the expression of AIRE up, down, or unchanged after chemical perturbation Alvocidib in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
## T... | null | unchanged | chemical | <thinking>Alvocidib inhibits CDK1, CDK7, PRKCE, PRKCD, and PRKDC, leading to reduced activation of RAF1 and TP53, respectively; however, CDK1 and CDK7 inhibition suppresses RAF1 and TP53, which normally activate AIRE, while PRKCE and PRKDC inhibition reduces TGFBR2 activation, which also promotes AIRE expression. Despi... |
B cells_Alvocidib_ANKFY1 | You are an expert biologist. Your goal is to determine: Is the expression of ANKFY1 up, down, or unchanged after chemical perturbation Alvocidib in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
##... | null | unchanged | chemical | <thinking>Alvocidib inhibits CDK4 and CDK9, both of which regulate BRCA1, and also inhibits GAK, which activates AR; however, BRCA1 and AR are both at low basal expression and directly regulate ANKFY1, with BRCA1 acting as a positive regulator and AR as a negative regulator. The inhibition of CDK4 and CDK9 reduces BRCA... |
B cells_Alvocidib_ANKMY2 | You are an expert biologist. Your goal is to determine: Is the expression of ANKMY2 up, down, or unchanged after chemical perturbation Alvocidib in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
##... | null | unchanged | chemical | <thinking>Alvocidib inhibits CAMKK1 and PRKCD, both of which activate EP300, and also inhibits CDK9, a regulator of ANKMY2; however, EP300 is activated through multiple parallel inputs—via CAMKK1, PRKCD, and CDK9—such that the net activation of EP300 remains stable despite the inhibition of these upstream components, d... |
B cells_Alvocidib_ARHGAP20 | You are an expert biologist. Your goal is to determine: Is the expression of ARHGAP20 up, down, or unchanged after chemical perturbation Alvocidib in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
... | null | unchanged | chemical | <thinking>Alvocidib inhibits CDK13 and CDK4, both of which activate PAK1, and also inhibits CDK9, which regulates ARHGAP20; however, PAK1 activates ARHGAP20, and CDK9 directly regulates ARHGAP20, creating two parallel pathways that could influence ARHGAP20 expression. Despite this, ARHGAP20 expression remains unchanged... |
B cells_Alvocidib_ATP1B1 | You are an expert biologist. Your goal is to determine: Is the expression of ATP1B1 up, down, or unchanged after chemical perturbation Alvocidib in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
##... | null | unchanged | chemical | <thinking>Alvocidib inhibits CDK9 and GSK3B, leading to reduced activation of AR and NR3C1, respectively; however, AR and NR3C1 both regulate ATP1B1, and given that ATP1B1 exhibits low basal expression, the downstream effect on ATP1B1 is minimal due to the low starting level and the absence of significant compensatory ... |
B cells_Alvocidib_BRI3BP | You are an expert biologist. Your goal is to determine: Is the expression of BRI3BP up, down, or unchanged after chemical perturbation Alvocidib in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
##... | null | unchanged | chemical | <thinking>Alvocidib inhibits CCND2 and CCND3, both of which normally activate CDK4; however, due to the low basal expression of CCND2 and CCND3, the reduction in their activity results in only a minimal decrease in CDK4 levels. CDK4, in turn, activates BRI3BP, but because BRI3BP is already expressed at low basal levels... |
B cells_Alvocidib_CAVIN2 | You are an expert biologist. Your goal is to determine: Is the expression of CAVIN2 up, down, or unchanged after chemical perturbation Alvocidib in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
##... | null | unchanged | chemical | <thinking>Alvocidib inhibits CDK9 and GSK3A, leading to reduced CDK9 activity and diminished activation of AR, while GSK3A inhibition relieves suppression of JUN, resulting in increased JUN levels. However, AR and JUN both regulate CAVIN2, with AR acting as a positive regulator and JUN as a negative regulator; the net ... |
B cells_Alvocidib_CBX4 | You are an expert biologist. Your goal is to determine: Is the expression of CBX4 up, down, or unchanged after chemical perturbation Alvocidib in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
## T... | null | unchanged | chemical | <thinking>Alvocidib inhibits CDK7 and CSNK1A1, leading to reduced activation of TP53 and STAT3, respectively; however, TP53 and STAT3 both contribute to the activation of CEBPB, and despite their inhibition, CEBPB remains at medium basal levels due to compensatory signaling through STAT1, which is activated by MAPK14 a... |
B cells_Alvocidib_CCND2 | You are an expert biologist. Your goal is to determine: Is the expression of CCND2 up, down, or unchanged after chemical perturbation Alvocidib in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
## ... | null | unchanged | chemical | <thinking>Alvocidib inhibits KDR, which reduces activation of STAT3, a transcription factor that normally promotes CCND2 expression; however, due to the low basal expression of CCND2, the pathway's output remains minimal even under reduced STAT3 activity, as the gene is already operating near its expression floor. The ... |
B cells_Alvocidib_CD8B2 | You are an expert biologist. Your goal is to determine: Is the expression of CD8B2 up, down, or unchanged after chemical perturbation Alvocidib in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
## ... | null | unchanged | chemical | <thinking>Alvocidib inhibits CDK7 and CDK9, leading to reduced activation of TP53 and STAT1, respectively; however, TP53 and STAT1 both contribute to the regulation of HLA-E, which in turn activates CD8B2, while NFKB1—activated by CDK9—also promotes CD8B2 expression. Despite these regulatory inputs, CD8B2 maintains low... |
B cells_Alvocidib_CDCP1 | You are an expert biologist. Your goal is to determine: Is the expression of CDCP1 up, down, or unchanged after chemical perturbation Alvocidib in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
## ... | null | unchanged | chemical | <thinking>Alvocidib inhibits GSK3A, PTK2, and PRKCD, all of which are known to regulate CDCP1, with GSK3A and PTK2 acting as positive regulators and PRKCD as a negative regulator; however, the basal expression of CDCP1 is low across all contexts, and the magnitude of regulation by each kinase is likely insufficient to ... |
B cells_Alvocidib_CENPO | You are an expert biologist. Your goal is to determine: Is the expression of CENPO up, down, or unchanged after chemical perturbation Alvocidib in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
## ... | null | unchanged | chemical | <thinking>Alvocidib inhibits CDK7 and CDK9, leading to reduced activation of TP53 and RB1, respectively; however, TP53 and RB1 both contribute to the activation of YY1, and YY1 in turn regulates CENPO. Despite the inhibition of upstream kinases, the basal expression of CENPO is low, and the pathway from CDK7/CDK9 to YY... |
B cells_Alvocidib_CHRNA10 | You are an expert biologist. Your goal is to determine: Is the expression of CHRNA10 up, down, or unchanged after chemical perturbation Alvocidib in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
#... | null | unchanged | chemical | <thinking>Alvocidib inhibits CDK5, CDK7, and PIM1, leading to reduced activation of GSK3B through both CDK5 and CDK7, while PIM1 inhibition further suppresses GSK3B activation. However, GSK3B is already at low basal expression and is a key regulator of CHRNA10, which itself is expressed at low levels in B cells. Despit... |
B cells_Alvocidib_CHRNG | You are an expert biologist. Your goal is to determine: Is the expression of CHRNG up, down, or unchanged after chemical perturbation Alvocidib in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
## ... | null | unchanged | chemical | <thinking>Alvocidib inhibits CDK7 and CDK9, leading to reduced activation of TP53 and diminished regulation of AR, respectively; however, TP53 activation is insufficient to significantly elevate YY1, which normally represses CHRNG, while AR, which activates CHRNG, remains unaltered due to the low basal expression of AR... |
B cells_Alvocidib_CHST13 | You are an expert biologist. Your goal is to determine: Is the expression of CHST13 up, down, or unchanged after chemical perturbation Alvocidib in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
##... | null | unchanged | chemical | <thinking>Alvocidib inhibits CDK7 and RPS6KA1, leading to reduced activation of TP53 and NFKB1, respectively; however, TP53 and NFKB1 both act as upstream activators of CHST13, and their basal activity is already low, resulting in minimal baseline induction of CHST13. Despite the inhibition of CDK7, which normally acti... |
B cells_Alvocidib_CLIC2 | You are an expert biologist. Your goal is to determine: Is the expression of CLIC2 up, down, or unchanged after chemical perturbation Alvocidib in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
## ... | null | unchanged | chemical | <thinking>Alvocidib inhibits CDK19 and CDK9, both of which activate STAT1, and inhibits GSK3B, which normally activates PRKCD; however, STAT1 and PRKCD both regulate CLIC2, and given that CLIC2 has low basal expression, the downstream effect on CLIC2 is minimal despite the perturbation. The inhibition of CDK19 and CDK9... |
B cells_Alvocidib_COQ4 | You are an expert biologist. Your goal is to determine: Is the expression of COQ4 up, down, or unchanged after chemical perturbation Alvocidib in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
## T... | null | unchanged | chemical | <thinking>Alvocidib inhibits CDK9 and GSK3A, leading to reduced activation of AR and ETS1, respectively; however, AR and ETS1 both regulate COQ4, and given that COQ4 exhibits low basal expression, the downstream effect on COQ4 is minimal due to the floor effect of its baseline level. Despite the inhibition of upstream ... |
B cells_Alvocidib_CPS1 | You are an expert biologist. Your goal is to determine: Is the expression of CPS1 up, down, or unchanged after chemical perturbation Alvocidib in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
## T... | null | unchanged | chemical | <thinking>Alvocidib inhibits GSK3A and GSK3B, leading to reduced suppression of JUN and STAT3, respectively; however, JUN and STAT3 both activate NR3C1, and NR3C1 in turn regulates CPS1. Despite the inhibition of GSK3A and GSK3B, the basal expression of CPS1 is low, and the activation of NR3C1 by both JUN and STAT3 is ... |
B cells_Alvocidib_CYB5B | You are an expert biologist. Your goal is to determine: Is the expression of CYB5B up, down, or unchanged after chemical perturbation Alvocidib in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
## ... | null | unchanged | chemical | <thinking>Alvocidib inhibits GSK3B, leading to reduced suppression of SREBF1, which would normally increase SREBF1 activity and subsequently elevate CYB5B expression; however, the basal expression of CYB5B is already low, and the pathway from SREBF1 to CYB5B operates under a weak regulatory influence, such that even wi... |
B cells_Alvocidib_DAP3 | You are an expert biologist. Your goal is to determine: Is the expression of DAP3 up, down, or unchanged after chemical perturbation Alvocidib in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
## T... | null | unchanged | chemical | <thinking>Alvocidib inhibits GSK3A and PRKCD, leading to reduced suppression of CTNNB1, which would normally be inhibited by GSK3A and activated by PRKCD; however, the basal expression of CTNNB1 is low, and the net effect of these opposing regulatory actions is balanced, resulting in minimal change in CTNNB1 levels. Si... |
B cells_Alvocidib_DDX52 | You are an expert biologist. Your goal is to determine: Is the expression of DDX52 up, down, or unchanged after chemical perturbation Alvocidib in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
## ... | null | unchanged | chemical | <thinking>Alvocidib inhibits CDK5 and CDK5R1, both of which activate ATM; however, ATM is already at medium basal expression, and its activation is partially offset by the inhibition of CDK6, which normally activates ATM, thereby maintaining a balanced level of ATM signaling. Since ATM regulates DDX52, and DDX52 is exp... |
B cells_Alvocidib_DOK2 | You are an expert biologist. Your goal is to determine: Is the expression of DOK2 up, down, or unchanged after chemical perturbation Alvocidib in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
## T... | null | unchanged | chemical | <thinking>Alvocidib inhibits CDK5 and CDK7, leading to reduced activation of JAK1 and TP53, respectively; however, JAK1 normally activates RAC1, and TP53 activates RHOA, both of which in turn activate DOK2, while PRKCQ also activates DOK2. Despite these upstream regulatory inputs, DOK2 maintains low basal expression, a... |
B cells_Alvocidib_DRD4 | You are an expert biologist. Your goal is to determine: Is the expression of DRD4 up, down, or unchanged after chemical perturbation Alvocidib in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
## T... | null | unchanged | chemical | <thinking>Alvocidib inhibits CDK9 and GAK, both of which are upstream regulators of AR; however, AR is already at low basal expression and is regulated by both CDK9 and GAK, meaning that inhibition of either kinase would be expected to reduce AR activity. Despite this, AR remains at low levels, and since AR directly re... |
B cells_Alvocidib_DST | You are an expert biologist. Your goal is to determine: Is the expression of DST up, down, or unchanged after chemical perturbation Alvocidib in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
## Ta... | null | unchanged | chemical | <thinking>Alvocidib inhibits CDK7 and GSK3A, leading to reduced activation of TP53 and CREB1, respectively; however, TP53 and CREB1 both act as positive regulators of DST, and their basal activity is already low, with DST maintaining a low basal expression level. Despite the inhibition of upstream activators, the minim... |
B cells_Alvocidib_DTHD1 | You are an expert biologist. Your goal is to determine: Is the expression of DTHD1 up, down, or unchanged after chemical perturbation Alvocidib in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
## ... | null | unchanged | chemical | <thinking>Alvocidib inhibits CDK1 and GSK3A, leading to reduced activation of JUN and JUND, respectively; however, JUN and JUND both regulate DTHD1, and given that DTHD1 exhibits low basal expression, the transcriptional output remains minimal regardless of fluctuations in upstream regulators. The inhibition of CDK1 di... |
B cells_Alvocidib_ECE1 | You are an expert biologist. Your goal is to determine: Is the expression of ECE1 up, down, or unchanged after chemical perturbation Alvocidib in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
## T... | null | unchanged | chemical | <thinking>Alvocidib inhibits CDK1 and CDK9, both of which regulate STAT3, leading to reduced STAT3 activity; however, STAT3 activates ECE1, and GSK3A, which is inhibited by CDK9, also regulates ECE1, suggesting a potential dual regulatory influence. Despite this, ECE1 maintains low basal expression, and the pathway inp... |
B cells_Alvocidib_ERC1 | You are an expert biologist. Your goal is to determine: Is the expression of ERC1 up, down, or unchanged after chemical perturbation Alvocidib in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
## T... | null | unchanged | chemical | <thinking>Alvocidib inhibits MAP4K2 and SQSTM1, both of which activate GSK3B, and also inhibits MAP3K1, which activates MAP4K2; however, GSK3B is already at low basal expression and is regulated by multiple upstream inputs, including MAP4K2 and SQSTM1, such that its activity remains stable despite perturbation. Since E... |
B cells_Alvocidib_ETS2 | You are an expert biologist. Your goal is to determine: Is the expression of ETS2 up, down, or unchanged after chemical perturbation Alvocidib in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
## T... | null | unchanged | chemical | <thinking>Alvocidib inhibits CDK2 and GSK3A, leading to reduced CDK2 activity and diminished GSK3A inhibition; CDK2 normally activates TP53, which in turn activates ETS2, while GSK3A inhibition would be expected to relieve suppression of JUN, a positive regulator of ETS2. However, the basal expression of ETS2 is low, a... |
B cells_Alvocidib_FBXO10 | You are an expert biologist. Your goal is to determine: Is the expression of FBXO10 up, down, or unchanged after chemical perturbation Alvocidib in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
##... | null | unchanged | chemical | <thinking>Alvocidib inhibits CDK9 and PIM2, leading to reduced activation of AR and MYC, respectively; however, AR and MYC both regulate FBXO10, and given that basal FBXO10 expression is low, the transcriptional input from either pathway is minimal. The inhibition of CDK9 reduces AR activity, while PIM2 inhibition redu... |
B cells_Alvocidib_FBXO30 | You are an expert biologist. Your goal is to determine: Is the expression of FBXO30 up, down, or unchanged after chemical perturbation Alvocidib in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
##... | null | unchanged | chemical | <thinking>Alvocidib inhibits CDK7 and GAK, leading to reduced activation of AR through both CDK7-mediated and GAK-mediated pathways; however, AR is already at low basal expression and exerts minimal regulatory influence on FBXO30, which is also expressed at low levels. Given that the basal expression of FBXO30 is low a... |
B cells_Alvocidib_FCRLB | You are an expert biologist. Your goal is to determine: Is the expression of FCRLB up, down, or unchanged after chemical perturbation Alvocidib in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
## ... | null | unchanged | chemical | <thinking>Alvocidib inhibits CDK9, GAK, and PRKCE, leading to reduced activation of AR and CREB1, respectively; however, AR and CREB1 both regulate FCRLB, and given that FCRLB exhibits low basal expression, the downstream effect on FCRLB is minimal due to the floor effect of low baseline activity. Despite the inhibitio... |
B cells_Alvocidib_FNTB | You are an expert biologist. Your goal is to determine: Is the expression of FNTB up, down, or unchanged after chemical perturbation Alvocidib in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
## T... | null | unchanged | chemical | <thinking>Alvocidib inhibits CDK7 and GSK3A, leading to reduced suppression of TP53 and diminished inhibition of HIF1A, respectively; however, TP53 activation would normally promote FNTB expression, while HIF1A inhibition would reduce FNTB expression, creating opposing regulatory forces. Given that FNTB exhibits low ba... |
B cells_Alvocidib_FRMD4A | You are an expert biologist. Your goal is to determine: Is the expression of FRMD4A up, down, or unchanged after chemical perturbation Alvocidib in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
##... | null | unchanged | chemical | <thinking>Alvocidib inhibits CDK9 and GAK, leading to reduced activation of AR and NFKB1, respectively; however, AR normally represses FRMD4A, and NFKB1 activates CTCF, which in turn regulates FRMD4A, creating a dual regulatory influence on FRMD4A expression. Despite this, FRMD4A maintains low basal expression, and the... |
B cells_Alvocidib_GALNT5 | You are an expert biologist. Your goal is to determine: Is the expression of GALNT5 up, down, or unchanged after chemical perturbation Alvocidib in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
##... | null | unchanged | chemical | <thinking>Alvocidib inhibits CDK5 and GSK3A, leading to reduced activation of JUN via CDK5 and reduced inhibition of JUN by GSK3A; however, JUN is already at medium basal levels, and its regulation by both CDK5 and GSK3A is counterbalanced such that the net effect on JUN activity remains stable. Since JUN directly regu... |
B cells_Alvocidib_GORASP1 | You are an expert biologist. Your goal is to determine: Is the expression of GORASP1 up, down, or unchanged after chemical perturbation Alvocidib in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
#... | null | unchanged | chemical | <thinking>Alvocidib inhibits CCNB1 and RPS6KA1, both of which activate MAPK1; however, MAPK1 is already at medium basal expression, and its activation is partially offset by the low basal levels of its upstream activators, which are themselves suppressed by the perturbation. Despite this, MAPK1 remains active due to re... |
B cells_Alvocidib_HCAR2 | You are an expert biologist. Your goal is to determine: Is the expression of HCAR2 up, down, or unchanged after chemical perturbation Alvocidib in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
## ... | null | unchanged | chemical | <thinking>Alvocidib inhibits CDK1, GSK3A, and PRKCQ, all of which are upstream regulators of STAT3; however, the basal expression of STAT3 is medium, and its activation is counterbalanced by the opposing effects of GSK3A (inhibitory) and PRKCQ (activating), resulting in a net stabilization of STAT3 activity despite per... |
B cells_Alvocidib_HIRIP3 | You are an expert biologist. Your goal is to determine: Is the expression of HIRIP3 up, down, or unchanged after chemical perturbation Alvocidib in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
##... | null | unchanged | chemical | <thinking>Alvocidib inhibits CDK7 and CDK2, both of which are known to regulate HIRIP3, with CDK7 exerting a positive regulatory influence and CDK2 acting as a negative regulator; however, due to the low basal expression of HIRIP3 and the opposing regulatory effects of CDK7 and CDK2, the net impact on HIRIP3 expression... |
B cells_Alvocidib_HMGCS1 | You are an expert biologist. Your goal is to determine: Is the expression of HMGCS1 up, down, or unchanged after chemical perturbation Alvocidib in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
##... | null | unchanged | chemical | <thinking>Alvocidib inhibits CDK1 and CDK5, both of which activate HDAC1; however, HDAC1 is already present at medium basal levels, and its inhibition would be expected to reduce HMGCS1 expression, which is normally low and regulated by HDAC1. Despite this, HMGCS1 expression remains unchanged because the basal level of... |
B cells_Alvocidib_HMGXB4 | You are an expert biologist. Your goal is to determine: Is the expression of HMGXB4 up, down, or unchanged after chemical perturbation Alvocidib in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
##... | null | unchanged | chemical | <thinking>Alvocidib inhibits CDK9 and GSK3B, both of which activate NFKB1, and also inhibits PRKCD, a regulator of NFKB1, while simultaneously inhibiting TYK2, another activator of NFKB1. Despite these inhibitory actions on upstream activators, NFKB1 remains at medium basal levels due to compensatory activation through... |
B cells_Alvocidib_HOXA1 | You are an expert biologist. Your goal is to determine: Is the expression of HOXA1 up, down, or unchanged after chemical perturbation Alvocidib in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
## ... | null | unchanged | chemical | <thinking>Alvocidib inhibits CDK13 and PLK1, leading to reduced activation of CCNB2 and diminished inhibition of SUZ12, respectively; however, CCNB2 regulates HOXA1, and SUZ12 also regulates HOXA1, creating a dual regulatory influence on HOXA1 expression. While CDK13 inhibition reduces CCNB2 activation, which would typ... |
B cells_Alvocidib_HSD17B1 | You are an expert biologist. Your goal is to determine: Is the expression of HSD17B1 up, down, or unchanged after chemical perturbation Alvocidib in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
#... | null | unchanged | chemical | <thinking>Alvocidib inhibits CDK9 and RPS6KA1, leading to reduced activation of NFKB1 and RELA, respectively; however, NFKB1 and RELA both activate HSD17B1, and given that basal HSD17B1 expression is low, the downstream effect of diminished upstream activation is minimal due to the gene's inherently low expression leve... |
B cells_Alvocidib_IGFBP3 | You are an expert biologist. Your goal is to determine: Is the expression of IGFBP3 up, down, or unchanged after chemical perturbation Alvocidib in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
##... | null | unchanged | chemical | <thinking>Alvocidib inhibits CDK7 and CDK9, leading to reduced activation of TP53 and diminished regulation of STAT3, respectively; however, TP53 activation is partially offset by the low basal expression of TP53, and the inhibition of CDK9 does not significantly alter STAT3 activity due to its medium basal level and p... |
B cells_Alvocidib_IL31RA | You are an expert biologist. Your goal is to determine: Is the expression of IL31RA up, down, or unchanged after chemical perturbation Alvocidib in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
##... | null | unchanged | chemical | <thinking>Alvocidib inhibits CDK2 and PIM1, both of which activate STAT3, and also inhibits GSK3B, a negative regulator of FOXP3; however, STAT3 activates FOXP3, and FOXP3 directly regulates IL31RA, while STAT3 also directly activates IL31RA. Despite these regulatory connections, IL31RA expression remains unchanged bec... |
B cells_Alvocidib_ILKAP | You are an expert biologist. Your goal is to determine: Is the expression of ILKAP up, down, or unchanged after chemical perturbation Alvocidib in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
## ... | null | unchanged | chemical | <thinking>Alvocidib inhibits PRKCE and RPS6KA1, both of which activate MAPK1, and also inhibits NOTCH1, which activates MAPK1; however, MAPK1 is already at medium basal expression, and its activation is maintained through multiple parallel inputs, including PRKCE, RPS6KA1, and NOTCH1, such that the net activation of MA... |
B cells_Alvocidib_KRT1 | You are an expert biologist. Your goal is to determine: Is the expression of KRT1 up, down, or unchanged after chemical perturbation Alvocidib in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
## T... | null | unchanged | chemical | <thinking>Alvocidib inhibits CDK9 and PRKCE, both of which are known to regulate KRT1 expression; however, given that KRT1 exhibits low basal expression in B cells, the transcriptional output remains unchanged despite the inhibition of its regulators. The low baseline level of KRT1 suggests a minimal dynamic range, suc... |
B cells_Alvocidib_LCORL | You are an expert biologist. Your goal is to determine: Is the expression of LCORL up, down, or unchanged after chemical perturbation Alvocidib in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
## ... | null | unchanged | chemical | <thinking>Alvocidib inhibits CDK1, CDK7, and GSK3A, leading to reduced activation of TP53 and E2F4, respectively; however, TP53 and E2F4 both act as transcriptional regulators of LCORL, and given that basal LCORL expression is low, the transcriptional output remains minimal regardless of changes in upstream regulators.... |
B cells_Alvocidib_MAP1A | You are an expert biologist. Your goal is to determine: Is the expression of MAP1A up, down, or unchanged after chemical perturbation Alvocidib in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
## ... | null | unchanged | chemical | <thinking>Alvocidib inhibits CDK2, DYRK1A, and GSK3B, all of which are known to regulate MAP1A, with CDK2 and DYRK1A acting as positive regulators and GSK3B as a negative regulator; however, due to the low basal expression of MAP1A and the presence of multiple regulatory inputs, the net effect on MAP1A expression is ne... |
B cells_Alvocidib_MFGE8 | You are an expert biologist. Your goal is to determine: Is the expression of MFGE8 up, down, or unchanged after chemical perturbation Alvocidib in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
## ... | null | unchanged | chemical | <thinking>Alvocidib inhibits CDK7 and CDK9, both of which regulate TP53, leading to reduced TP53 activity; however, TP53 is already at low basal expression and its inhibition does not significantly alter the downstream activation of MFGE8, which is directly activated by EP300 and GSK3A. While CDK9 inhibition would be e... |
B cells_Alvocidib_MYZAP | You are an expert biologist. Your goal is to determine: Is the expression of MYZAP up, down, or unchanged after chemical perturbation Alvocidib in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
## ... | null | unchanged | chemical | <thinking>Alvocidib inhibits CDK7 and GSK3A, leading to reduced activation of TP53 and diminished inhibition of MYC, respectively; however, TP53 activation is weak due to low basal expression and the inhibitory effect of GSK3A on MYC, which counteracts the loss of CDK7-mediated TP53 activation. Despite this, MYC remain... |
B cells_Alvocidib_NME2 | You are an expert biologist. Your goal is to determine: Is the expression of NME2 up, down, or unchanged after chemical perturbation Alvocidib in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
## T... | null | unchanged | chemical | <thinking>Alvocidib inhibits CDK1 and GSK3A, leading to reduced CDK1 activity and reduced GSK3A activity; CDK1 normally activates MYC, and GSK3A normally inhibits MYC, so the inhibition of CDK1 and GSK3A results in a net decrease in MYC activation due to opposing effects that balance each other, maintaining MYC at low ... |
B cells_Alvocidib_NPHP1 | You are an expert biologist. Your goal is to determine: Is the expression of NPHP1 up, down, or unchanged after chemical perturbation Alvocidib in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
## ... | null | unchanged | chemical | <thinking>Alvocidib inhibits CDK13, CSNK2A1, PTK2B, and PRKCE, all of which are known to regulate AR, with CDK13, CSNK2A1, and PTK2B acting as positive regulators and PRKCE as a negative regulator; however, the basal expression of AR is low, and the net effect of these opposing regulatory inputs is balanced, resulting ... |
B cells_Alvocidib_PEX5L | You are an expert biologist. Your goal is to determine: Is the expression of PEX5L up, down, or unchanged after chemical perturbation Alvocidib in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
## ... | null | unchanged | chemical | <thinking>Alvocidib inhibits CAMKK1 and PRKCE, both of which activate EP300, and also inhibits RAF1, which activates CDK9; however, EP300 and CDK9 both regulate PEX5L, and given that PEX5L exhibits low basal expression, the transcriptional output remains minimal regardless of upstream modulation. The inhibition of upst... |
B cells_Alvocidib_PGGHG | You are an expert biologist. Your goal is to determine: Is the expression of PGGHG up, down, or unchanged after chemical perturbation Alvocidib in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
## ... | null | unchanged | chemical | <thinking>Alvocidib inhibits CDK2 and PIM1, both of which activate STAT3, and also inhibits GSK3B, a negative regulator of FOXP3; however, STAT3 activates FOXP3, and FOXP3 directly regulates PGGHG, while STAT3 also activates PGGHG, creating parallel positive inputs to PGGHG expression. Despite the inhibition of upstrea... |
B cells_Alvocidib_PROSER1 | You are an expert biologist. Your goal is to determine: Is the expression of PROSER1 up, down, or unchanged after chemical perturbation Alvocidib in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
#... | null | unchanged | chemical | <thinking>Alvocidib inhibits GSK3B, which normally suppresses FOXP3; however, FOXP3 is already at low basal expression and exerts weak regulation on PROSER1, which is also expressed at low levels. Given that the inhibition of GSK3B would be expected to increase FOXP3, the resulting upregulation of FOXP3 would only mode... |
B cells_Alvocidib_PRPS1 | You are an expert biologist. Your goal is to determine: Is the expression of PRPS1 up, down, or unchanged after chemical perturbation Alvocidib in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
## ... | null | unchanged | chemical | <thinking>Alvocidib inhibits CDK1 and CDK9, both of which regulate AR; however, AR is already at low basal expression and exerts weak activation of PRPS1, which is itself expressed at low levels. Despite the inhibition of CDK1 and CDK9, the reduction in AR activity is insufficient to significantly alter PRPS1 expressio... |
B cells_Alvocidib_PRX | You are an expert biologist. Your goal is to determine: Is the expression of PRX up, down, or unchanged after chemical perturbation Alvocidib in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
## Ta... | null | unchanged | chemical | <thinking>Alvocidib inhibits CDK5, GSK3B, and PRKCE, all of which are upstream regulators of NFE2L2; however, CDK5 and GSK3B exert inhibitory effects on NFE2L2, while PRKCE activates it, resulting in a net balance that maintains NFE2L2 expression at medium levels despite perturbation. Since NFE2L2 is a direct activator... |
B cells_Alvocidib_PTGDR | You are an expert biologist. Your goal is to determine: Is the expression of PTGDR up, down, or unchanged after chemical perturbation Alvocidib in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
## ... | null | unchanged | chemical | <thinking>Alvocidib inhibits CDK7 and CDK9, leading to reduced activation of TP53 and NFKB1, respectively; however, TP53 and NFKB1 both exert inhibitory effects on MYC, and since MYC is already at low basal levels, the downstream suppression of MYC is minimal. Given that MYC is a key activator of PTGDR and PTGDR is exp... |
B cells_Alvocidib_PTPRCAP | You are an expert biologist. Your goal is to determine: Is the expression of PTPRCAP up, down, or unchanged after chemical perturbation Alvocidib in B cells?
Answer the question based on the context. You must reason using your own knowledge on the biological pathway that connects the perturbation to the effect gene.
#... | null | unchanged | chemical | <thinking>Alvocidib inhibits CDK5, RPS6KA1, and PRKCE, leading to reduced activation of RHOA and MAPK1/MAPK3, which in turn would be expected to suppress PTPRCAP expression through both RHOA and MAPK1/MAPK3-mediated regulation. However, PTPRCAP exhibits low basal expression, and the inhibitory effects on upstream activ... |
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