CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At2g38560

Gene name TFIIS (TRANSCRIPT ELONGATION FACTOR IIS)

Module size 34 genes

NF 0.38

%ile 51.4

Co-expression network

: Transcription factor, : Binding protein, : Enzyme protein, : Other protein
: VF over 0.50, : over 0.25, : below 0.25

Co-expressed genes

Click gene/probe ID to show a list of genes that are co-expressed with the gene.

VF %ile CC Gene ID Repr. ID Gene name Func. O.I. H.G. S.X. Other DB
1.00 100.0 1.00 At2g38560 818438 TFIIS (TRANSCRIPT ELONGATION FACTOR IIS) Encodes RNA polymerase II transcript elongation factor TFIIS. Complements yeast TFIIS mutation. Mutant plants display essentially normal development, but they flower slightly earlier than the wild type and show clearly reduced seed dormancy. O.I. H.G. S.X.
0.62 77.3 0.94 At5g64200 836541 ATSC35 encodes an SC35-like splicing factor of 35 kD localized to the nuclear specks. O.I. H.G. S.X.
0.55 70.6 0.94 At5g04280 830307 glycine-rich RNA-binding protein F:RNA binding, zinc ion binding, nucleotide binding, nucleic acid binding;P:biological_process unknown;C:nucleolus;MPFOBVA O.I. H.G. S.X.
0.50 65.3 0.93 At5g52040 835279 ATRSP41 encodes an arginine/serine-rich splicing factor. transcript is alternatively spliced and is differentially expressed in different tissues (flowers, roots, stems, and leaves) examined. O.I. H.G. S.X.
0.47 61.2 0.94 At5g11170 830986 ATP binding / ATP-dependent helicase/ helicase/ nucleic acid binding F:helicase activity, ATP-dependent helicase activity, nucleic acid binding, ATP binding;P:response to cadmium ion;C:nucleolus;BOMFPAV O.I. H.G. S.X.
0.46 59.8 0.93 At4g39520 830106 GTP-binding protein, putative F:GTP binding;P:unknown;C:intracellular;BOMAFP O.I. H.G. S.X.
0.46 59.8 0.93 At5g50320 835098 ELO3 (ELONGATA 3) A subunit of Elongator, a histone acetyl transferase complex, consisting of six subunits (ELP1�ELP6), that copurifies with the elongating RNAPII in yeast and humans. Three Arabidopsis thaliana genes, encoding homologs of the yeast Elongator subunits ELP1, ELP3 (histone acetyl transferase), and ELP4 are responsible for the narrow leaf phenotype in elongata mutants and for reduced root growth that results from a decreased cell division rate. Two lines with RNAi constructs directed against HAG3 grow normally and can produce root calli, but have defects in agrobacterium-mediated transformation. O.I. H.G. S.X.
0.44 57.2 0.94 At2g43770 818980 transducin family protein / WD-40 repeat family protein F:nucleotide binding;P:biological_process unknown;C:CUL4 RING ubiquitin ligase complex, heterotrimeric G-protein complex;MFOBPAV O.I. H.G. S.X.
0.42 53.9 0.93 At5g27540 832814 MIRO1 (Miro-related GTP-ase 1) Encodes a protein with similarity to GTPases that is localized to the mitochondrion. Involved in embryogenesis, pollen tube growth and required for mitochondrial development. O.I. H.G. S.X.
0.41 52.4 0.93 At1g65650 842876 UCH2 F:ubiquitin-specific protease activity, ubiquitin thiolesterase activity;P:protein deubiquitination, shoot development, shoot morphogenesis, leaf development, ubiquitin-dependent protein catabolic process;C:nucleus, intracellular, cytoplasm;MFOP O.I. H.G. S.X.
0.39 48.4 0.93 At1g04510 839503 transducin family protein / WD-40 repeat family protein F:ubiquitin-protein ligase activity, nucleotide binding;P:response to cadmium ion;C:nucleolus, CUL4 RING ubiquitin ligase complex;MFOBPA O.I. H.G. S.X.
0.39 48.4 0.94 At4g19210 827661 ATRLI2 member of RLI subfamily O.I. H.G. S.X.
0.39 48.4 0.93 At2g25970 817137 KH domain-containing protein F:RNA binding, nucleic acid binding;P:unknown;C:unknown;MBFOPVA O.I. H.G. S.X.
0.38 46.7 0.94 At3g59990 825169 MAP2B (METHIONINE AMINOPEPTIDASE 2B) Encodes a MAP2 like methionine aminopeptidase O.I. H.G. S.X.
0.37 45.0 0.94 At3g19760 821513 eukaryotic translation initiation factor 4A, putative / eIF-4A, putative / DEAD box RNA helicase, putative F:helicase activity, ATP binding, ATP-dependent helicase activity, nucleic acid binding;P:unknown;C:nucleolus, nucleus, membrane;BOMFPAV O.I. H.G. S.X.
0.37 45.0 0.93 At5g02530 831923 RNA and export factor-binding protein, putative F:nucleotide binding, nucleic acid binding;P:biological_process unknown;C:cellular_component unknown;MFOPBVA O.I. H.G. S.X.
0.36 43.6 0.93 At3g49430 824105 SRp34a (Ser/Arg-rich protein 34a) F:RNA binding, nucleotide binding, nucleic acid binding;P:RNA splicing;C:nucleolus;MOPFBVA O.I. H.G. S.X.
0.36 43.6 0.94 At2g44020 819007 mitochondrial transcription termination factor-related / mTERF-related F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMO O.I. H.G. S.X.
0.36 43.6 0.94 At5g20920 832216 EIF2 BETA protein synthesis initiation factor eIF2 beta O.I. H.G. S.X.
0.35 41.6 0.93 At3g02200 821267 proteasome family protein F:molecular_function unknown;P:unknown;C:unknown;MFPOB O.I. H.G. S.X.
0.34 39.8 0.93 At3g07300 819918 eukaryotic translation initiation factor 2B family protein / eIF-2B family protein F:GTP binding, translation initiation factor activity;P:translational initiation, cellular metabolic process;C:eukaryotic translation initiation factor 2B complex;OBMFAP O.I. H.G. S.X.
0.34 39.8 0.93 At1g10840 837627 TIF3H1 Encodes eukaryotic initiation factor 3H1 subunit (TIF3H1). O.I. H.G. S.X.
0.33 38.1 0.93 At2g34970 818061 eIF4-gamma/eIF5/eIF2-epsilon domain-containing protein F:binding, transferase activity, translation initiation factor activity, nucleotidyltransferase activity;P:biosynthetic process, regulation of translational initiation;C:unknown;BOMAFP O.I. H.G. S.X.
0.33 38.1 0.93 At3g55000 824665 TON1A (TONNEAU 1) Encodes a protein of unknown function that is involved in cortical microtubule organization. Mutants exhibit abnormal cell growth and patterns of division. TON1A can functionally complement TON1B and their roles appear to be redundant in plants. Encodes a novel protein that is similar to human FOP and OFD1 centrosomal proteins. Localizes to the preprophase band, cytoplasm and cell cortex where it is probably associated with the cortical cytoskeleton. TON1A associates with plant centrins CEN1 and CEN2. O.I. H.G. S.X.
0.33 38.1 0.93 At4g11790 826785 Ran-binding protein 1 domain-containing protein / RanBP1 domain-containing protein F:molecular_function unknown;P:intracellular transport;C:cellular_component unknown;OMBFPVA O.I. H.G. S.X.
0.32 35.7 0.93 At5g64960 836620 CDKC2 (Cyclin dependent kinase group C 2) Encodes CDKC;2, part of a CDKC kinase complex that is targeted by Cauliflower mosaic virus (CaMV) for transcriptional activation of viral genes. Also regulates plant growth and development. Co-localizes with spliceosomal components in a manner dependent on the transcriptional status of the cells and on CDKC2-kinase activity. Expression of CDKC2 modifies the location of spliceosomal components. O.I. H.G. S.X.
0.31 33.8 0.93 At4g30890 829213 UBP24 (UBIQUITIN-SPECIFIC PROTEASE 24) Encodes a ubiquitin-specific protease. O.I. H.G. S.X.
0.31 33.8 0.93 At3g12130 820388 KH domain-containing protein / zinc finger (CCCH type) family protein F:transcription factor activity, nucleic acid binding;P:regulation of transcription;C:unknown;MPOFB O.I. H.G. S.X.
0.31 33.8 0.93 At5g45620 834602 26S proteasome regulatory subunit, putative (RPN9) F:molecular_function unknown;P:ubiquitin-dependent protein catabolic process;C:proteasome regulatory particle, lid subcomplex;MFOP O.I. H.G. S.X.
0.30 32.1 0.94 At2g39990 818587 EIF2 translation initiation factor eIF2 p47 subunit homolog O.I. H.G. S.X.
0.26 24.4 0.93 At3g02220 821238 unknown protein F:unknown;P:biological_process unknown;C:cellular_component unknown;MOPFBA O.I. H.G. S.X.
0.25 22.6 0.93 At1g72550 843587 tRNA synthetase beta subunit family protein F:phenylalanine-tRNA ligase activity, RNA binding, magnesium ion binding, nucleotide binding, ATP binding;P:phenylalanyl-tRNA aminoacylation, translation;C:phenylalanine-tRNA ligase complex, cytoplasm;BOMAFP O.I. H.G. S.X.
0.23 19.3 0.94 At3g57290 824896 EIF3E (EUKARYOTIC TRANSLATION INITIATION FACTOR 3E) Encodes a protein that is found in not only the eif3 complex but also in association with subunits of the COP9 signalosome. eIF3e appears to be subjected to proteasome-dependent degradation that requires the PCI domain of eIF3e. The level of eIF3e present in cells appears to affect the rate of translation. O.I. H.G. S.X.
0.21 15.8 0.93 At5g05780 830463 RPN8A (RP NON-ATPASE SUBUNIT 8A) Encodes a putative 26S proteasome subunit RPN8a. The function of RPN8a and other 26S subunits may be required for specifying leaf adaxial identity. O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
1.00	100.0	1.00	At2g38560	818438	TFIIS (TRANSCRIPT ELONGATION FACTOR IIS)	Encodes RNA polymerase II transcript elongation factor TFIIS. Complements yeast TFIIS mutation. Mutant plants display essentially normal development, but they flower slightly earlier than the wild type and show clearly reduced seed dormancy.	O.I.	H.G.	S.X.
0.62	77.3	0.94	At5g64200	836541	ATSC35	encodes an SC35-like splicing factor of 35 kD localized to the nuclear specks.	O.I.	H.G.	S.X.
0.55	70.6	0.94	At5g04280	830307	glycine-rich RNA-binding protein	F:RNA binding, zinc ion binding, nucleotide binding, nucleic acid binding;P:biological_process unknown;C:nucleolus;MPFOBVA	O.I.	H.G.	S.X.
0.50	65.3	0.93	At5g52040	835279	ATRSP41	encodes an arginine/serine-rich splicing factor. transcript is alternatively spliced and is differentially expressed in different tissues (flowers, roots, stems, and leaves) examined.	O.I.	H.G.	S.X.
0.47	61.2	0.94	At5g11170	830986	ATP binding / ATP-dependent helicase/ helicase/ nucleic acid binding	F:helicase activity, ATP-dependent helicase activity, nucleic acid binding, ATP binding;P:response to cadmium ion;C:nucleolus;BOMFPAV	O.I.	H.G.	S.X.
0.46	59.8	0.93	At4g39520	830106	GTP-binding protein, putative	F:GTP binding;P:unknown;C:intracellular;BOMAFP	O.I.	H.G.	S.X.
0.46	59.8	0.93	At5g50320	835098	ELO3 (ELONGATA 3)	A subunit of Elongator, a histone acetyl transferase complex, consisting of six subunits (ELP1�ELP6), that copurifies with the elongating RNAPII in yeast and humans. Three Arabidopsis thaliana genes, encoding homologs of the yeast Elongator subunits ELP1, ELP3 (histone acetyl transferase), and ELP4 are responsible for the narrow leaf phenotype in elongata mutants and for reduced root growth that results from a decreased cell division rate. Two lines with RNAi constructs directed against HAG3 grow normally and can produce root calli, but have defects in agrobacterium-mediated transformation.	O.I.	H.G.	S.X.
0.44	57.2	0.94	At2g43770	818980	transducin family protein / WD-40 repeat family protein	F:nucleotide binding;P:biological_process unknown;C:CUL4 RING ubiquitin ligase complex, heterotrimeric G-protein complex;MFOBPAV	O.I.	H.G.	S.X.
0.42	53.9	0.93	At5g27540	832814	MIRO1 (Miro-related GTP-ase 1)	Encodes a protein with similarity to GTPases that is localized to the mitochondrion. Involved in embryogenesis, pollen tube growth and required for mitochondrial development.	O.I.	H.G.	S.X.
0.41	52.4	0.93	At1g65650	842876	UCH2	F:ubiquitin-specific protease activity, ubiquitin thiolesterase activity;P:protein deubiquitination, shoot development, shoot morphogenesis, leaf development, ubiquitin-dependent protein catabolic process;C:nucleus, intracellular, cytoplasm;MFOP	O.I.	H.G.	S.X.
0.39	48.4	0.93	At1g04510	839503	transducin family protein / WD-40 repeat family protein	F:ubiquitin-protein ligase activity, nucleotide binding;P:response to cadmium ion;C:nucleolus, CUL4 RING ubiquitin ligase complex;MFOBPA	O.I.	H.G.	S.X.
0.39	48.4	0.94	At4g19210	827661	ATRLI2	member of RLI subfamily	O.I.	H.G.	S.X.
0.39	48.4	0.93	At2g25970	817137	KH domain-containing protein	F:RNA binding, nucleic acid binding;P:unknown;C:unknown;MBFOPVA	O.I.	H.G.	S.X.
0.38	46.7	0.94	At3g59990	825169	MAP2B (METHIONINE AMINOPEPTIDASE 2B)	Encodes a MAP2 like methionine aminopeptidase	O.I.	H.G.	S.X.
0.37	45.0	0.94	At3g19760	821513	eukaryotic translation initiation factor 4A, putative / eIF-4A, putative / DEAD box RNA helicase, putative	F:helicase activity, ATP binding, ATP-dependent helicase activity, nucleic acid binding;P:unknown;C:nucleolus, nucleus, membrane;BOMFPAV	O.I.	H.G.	S.X.
0.37	45.0	0.93	At5g02530	831923	RNA and export factor-binding protein, putative	F:nucleotide binding, nucleic acid binding;P:biological_process unknown;C:cellular_component unknown;MFOPBVA	O.I.	H.G.	S.X.
0.36	43.6	0.93	At3g49430	824105	SRp34a (Ser/Arg-rich protein 34a)	F:RNA binding, nucleotide binding, nucleic acid binding;P:RNA splicing;C:nucleolus;MOPFBVA	O.I.	H.G.	S.X.
0.36	43.6	0.94	At2g44020	819007	mitochondrial transcription termination factor-related / mTERF-related	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMO	O.I.	H.G.	S.X.
0.36	43.6	0.94	At5g20920	832216	EIF2 BETA	protein synthesis initiation factor eIF2 beta	O.I.	H.G.	S.X.
0.35	41.6	0.93	At3g02200	821267	proteasome family protein	F:molecular_function unknown;P:unknown;C:unknown;MFPOB	O.I.	H.G.	S.X.
0.34	39.8	0.93	At3g07300	819918	eukaryotic translation initiation factor 2B family protein / eIF-2B family protein	F:GTP binding, translation initiation factor activity;P:translational initiation, cellular metabolic process;C:eukaryotic translation initiation factor 2B complex;OBMFAP	O.I.	H.G.	S.X.
0.34	39.8	0.93	At1g10840	837627	TIF3H1	Encodes eukaryotic initiation factor 3H1 subunit (TIF3H1).	O.I.	H.G.	S.X.
0.33	38.1	0.93	At2g34970	818061	eIF4-gamma/eIF5/eIF2-epsilon domain-containing protein	F:binding, transferase activity, translation initiation factor activity, nucleotidyltransferase activity;P:biosynthetic process, regulation of translational initiation;C:unknown;BOMAFP	O.I.	H.G.	S.X.
0.33	38.1	0.93	At3g55000	824665	TON1A (TONNEAU 1)	Encodes a protein of unknown function that is involved in cortical microtubule organization. Mutants exhibit abnormal cell growth and patterns of division. TON1A can functionally complement TON1B and their roles appear to be redundant in plants. Encodes a novel protein that is similar to human FOP and OFD1 centrosomal proteins. Localizes to the preprophase band, cytoplasm and cell cortex where it is probably associated with the cortical cytoskeleton. TON1A associates with plant centrins CEN1 and CEN2.	O.I.	H.G.	S.X.
0.33	38.1	0.93	At4g11790	826785	Ran-binding protein 1 domain-containing protein / RanBP1 domain-containing protein	F:molecular_function unknown;P:intracellular transport;C:cellular_component unknown;OMBFPVA	O.I.	H.G.	S.X.
0.32	35.7	0.93	At5g64960	836620	CDKC2 (Cyclin dependent kinase group C 2)	Encodes CDKC;2, part of a CDKC kinase complex that is targeted by Cauliflower mosaic virus (CaMV) for transcriptional activation of viral genes. Also regulates plant growth and development. Co-localizes with spliceosomal components in a manner dependent on the transcriptional status of the cells and on CDKC2-kinase activity. Expression of CDKC2 modifies the location of spliceosomal components.	O.I.	H.G.	S.X.
0.31	33.8	0.93	At4g30890	829213	UBP24 (UBIQUITIN-SPECIFIC PROTEASE 24)	Encodes a ubiquitin-specific protease.	O.I.	H.G.	S.X.
0.31	33.8	0.93	At3g12130	820388	KH domain-containing protein / zinc finger (CCCH type) family protein	F:transcription factor activity, nucleic acid binding;P:regulation of transcription;C:unknown;MPOFB	O.I.	H.G.	S.X.
0.31	33.8	0.93	At5g45620	834602	26S proteasome regulatory subunit, putative (RPN9)	F:molecular_function unknown;P:ubiquitin-dependent protein catabolic process;C:proteasome regulatory particle, lid subcomplex;MFOP	O.I.	H.G.	S.X.
0.30	32.1	0.94	At2g39990	818587	EIF2	translation initiation factor eIF2 p47 subunit homolog	O.I.	H.G.	S.X.
0.26	24.4	0.93	At3g02220	821238	unknown protein	F:unknown;P:biological_process unknown;C:cellular_component unknown;MOPFBA	O.I.	H.G.	S.X.
0.25	22.6	0.93	At1g72550	843587	tRNA synthetase beta subunit family protein	F:phenylalanine-tRNA ligase activity, RNA binding, magnesium ion binding, nucleotide binding, ATP binding;P:phenylalanyl-tRNA aminoacylation, translation;C:phenylalanine-tRNA ligase complex, cytoplasm;BOMAFP	O.I.	H.G.	S.X.
0.23	19.3	0.94	At3g57290	824896	EIF3E (EUKARYOTIC TRANSLATION INITIATION FACTOR 3E)	Encodes a protein that is found in not only the eif3 complex but also in association with subunits of the COP9 signalosome. eIF3e appears to be subjected to proteasome-dependent degradation that requires the PCI domain of eIF3e. The level of eIF3e present in cells appears to affect the rate of translation.	O.I.	H.G.	S.X.
0.21	15.8	0.93	At5g05780	830463	RPN8A (RP NON-ATPASE SUBUNIT 8A)	Encodes a putative 26S proteasome subunit RPN8a. The function of RPN8a and other 26S subunits may be required for specifying leaf adaxial identity.	O.I.	H.G.	S.X.

Click More genes

Link to AtGenExpress Visualization Tool

Specific experiments for the module

Std2 GX %ile GSM ID Assay name GSE ID Experiment title Link to GEO
93.5 99.9 GSM184556 Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
58.9 99.8 GSM205432 Col_ leaf_ wildtype_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
56.3 99.8 GSM205428 met1-3_leaf_fourth-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
55.9 99.8 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
55.5 99.8 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
53.4 99.8 GSM205430 met1-3_leaf_fourth-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
53.2 99.8 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
51.6 99.8 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
49.4 99.8 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
48.3 99.8 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
46.4 99.8 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
45.8 99.8 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
44.5 99.8 GSM205426 met1-3_leaf_second-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
44.4 99.8 GSM205364 met1-3_leaf_second-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
44.0 99.8 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
43.5 99.8 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
42.4 99.8 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
41.3 99.8 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
40.5 99.8 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
38.7 99.8 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
38.3 99.8 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
37.8 99.8 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
37.5 99.7 GSM205435 Col_ leaf_ wildtype_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
36.2 99.7 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
35.1 99.7 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
29.9 99.7 GSM184551 Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
24.5 99.6 GSM311275 Laser capture microdissected (LCM) micropylar endosperm at the pre-globular stage, biological replicate 1 GSE12402 Expression data from Arabidopsis seed compartments at the pre-globular stage
23.2 99.6 GSM311276 Laser capture microdissected (LCM) micropylar endospermr at the pre-globular stage, biological replicate 2 GSE12402 Expression data from Arabidopsis seed compartments at the pre-globular stage
21.2 99.6 GSM133762 Lindsey_1-14_torpedo-root_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
15.5 99.5 E-MEXP-1138-raw-cel-1432773258
15.3 99.4 E-MEXP-1138-raw-cel-1432773290
13.6 99.4 GSM284389 Arabidopsis GMPE2 GSE11262 Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
12.0 99.3 GSM284394 Arabidopsis GCE3 GSE11262 Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
11.8 99.3 GSM184923 Arabidopsis, root cells, protophloem, 140 mM NaCl, replicate 2 GSE7641 Expression analysis of root cell-types after treatment with salt
11.5 99.3 E-MEXP-1138-raw-cel-1432773322
11.1 99.2 GSM226530 LCOLUMELLASB GSE8934 A high resolution organ expression map reveals novel expression patterns and predicts cellular function
10.8 99.2 GSM284391 Arabidopsis GPE3 GSE11262 Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
9.9 99.1 GSM284388 Arabidopsis GMPE1 GSE11262 Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
9.6 99.1 GSM133962 Fukuda_1-7_6A_Rep1_ATH1 GSE5748 In vitro tracheary element transdifferentiation of Col-0 suspension cells.
9.0 99.1 GSM176876 AWP_AL_Txed_1 GSE7334 Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
8.9 99.0 GSM133963 Fukuda_1-8_6B_Rep2_ATH1 GSE5748 In vitro tracheary element transdifferentiation of Col-0 suspension cells.
8.9 99.0 E-MEXP-1138-raw-cel-1432773066

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
93.5	99.9	GSM184556	Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
58.9	99.8	GSM205432	Col_ leaf_ wildtype_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
56.3	99.8	GSM205428	met1-3_leaf_fourth-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
55.9	99.8	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
55.5	99.8	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
53.4	99.8	GSM205430	met1-3_leaf_fourth-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
53.2	99.8	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
51.6	99.8	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
49.4	99.8	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
48.3	99.8	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
46.4	99.8	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
45.8	99.8	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
44.5	99.8	GSM205426	met1-3_leaf_second-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
44.4	99.8	GSM205364	met1-3_leaf_second-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
44.0	99.8	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
43.5	99.8	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
42.4	99.8	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
41.3	99.8	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
40.5	99.8	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
38.7	99.8	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
38.3	99.8	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
37.8	99.8	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
37.5	99.7	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
36.2	99.7	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
35.1	99.7	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
29.9	99.7	GSM184551	Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
24.5	99.6	GSM311275	Laser capture microdissected (LCM) micropylar endosperm at the pre-globular stage, biological replicate 1	GSE12402	Expression data from Arabidopsis seed compartments at the pre-globular stage
23.2	99.6	GSM311276	Laser capture microdissected (LCM) micropylar endospermr at the pre-globular stage, biological replicate 2	GSE12402	Expression data from Arabidopsis seed compartments at the pre-globular stage
21.2	99.6	GSM133762	Lindsey_1-14_torpedo-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
15.5	99.5	E-MEXP-1138-raw-cel-1432773258
15.3	99.4	E-MEXP-1138-raw-cel-1432773290
13.6	99.4	GSM284389	Arabidopsis GMPE2	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
12.0	99.3	GSM284394	Arabidopsis GCE3	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
11.8	99.3	GSM184923	Arabidopsis, root cells, protophloem, 140 mM NaCl, replicate 2	GSE7641	Expression analysis of root cell-types after treatment with salt
11.5	99.3	E-MEXP-1138-raw-cel-1432773322
11.1	99.2	GSM226530	LCOLUMELLASB	GSE8934	A high resolution organ expression map reveals novel expression patterns and predicts cellular function
10.8	99.2	GSM284391	Arabidopsis GPE3	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
9.9	99.1	GSM284388	Arabidopsis GMPE1	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
9.6	99.1	GSM133962	Fukuda_1-7_6A_Rep1_ATH1	GSE5748	In vitro tracheary element transdifferentiation of Col-0 suspension cells.
9.0	99.1	GSM176876	AWP_AL_Txed_1	GSE7334	Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
8.9	99.0	GSM133963	Fukuda_1-8_6B_Rep2_ATH1	GSE5748	In vitro tracheary element transdifferentiation of Col-0 suspension cells.
8.9	99.0	E-MEXP-1138-raw-cel-1432773066

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.082 3 GO:0008380 The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA.
0.076 4 GO:0006413 The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA, and an initiation complex that contains the first aminoacyl-tRNA.
0.069 2 GO:0006397 Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.

SF	Genes	GO ID	Process Name
0.082	3	GO:0008380	The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA.
0.076	4	GO:0006413	The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA, and an initiation complex that contains the first aminoacyl-tRNA.
0.069	2	GO:0006397	Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.

KEGG PATHWAY inferred to related to the module

SF Genes KEGG ID Pathway name Link to KEGG
0.043 2 03050 Proteasome
0.025 1 00970 Aminoacyl-tRNA biosynthesis
0.015 1 04120 Ubiquitin mediated proteolysis

SF	Genes	KEGG ID	Pathway name
0.043	2	03050	Proteasome
0.025	1	00970	Aminoacyl-tRNA biosynthesis
0.015	1	04120	Ubiquitin mediated proteolysis

Inter-species module comparison

Select a plant to compare co-expressed genes between species.
Glycine_max
Hordeum_vulgare
Oryza_sativa
Populus_trichocarpa
Triticum_aestivum
Vitis_vinifera
Zea_mays

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Gene ID	At2g38560
Gene name	TFIIS (TRANSCRIPT ELONGATION FACTOR IIS)
Module size	34 genes
NF	0.38
%ile	51.4

Co-expression analysis

Gene ID At2g38560 Gene name TFIIS (TRANSCRIPT ELONGATION FACTOR IIS) Module size 34 genes NF 0.38 %ile 51.4

Co-expression network

: Transcription factor, : Binding protein, : Enzyme protein, : Other protein: VF over 0.50, : over 0.25, : below 0.25

Co-expressed genes

Click More genes

Link to AtGenExpress Visualization Tool

Specific experiments for the module

Biological processes inferred to relate to the module

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG0.043203050Proteasome0.025100970Aminoacyl-tRNA biosynthesis0.015104120Ubiquitin mediated proteolysis

Inter-species module comparison

Select a plant to compare co-expressed genes between species.Glycine_maxHordeum_vulgareOryza_sativaPopulus_trichocarpaTriticum_aestivumVitis_viniferaZea_mays

Gene ID At2g38560

Gene name TFIIS (TRANSCRIPT ELONGATION FACTOR IIS)

Module size 34 genes

NF 0.38

%ile 51.4

: Transcription factor, : Binding protein, : Enzyme protein, : Other protein
: VF over 0.50, : over 0.25, : below 0.25

SF Genes KEGG ID Pathway name Link to KEGG
0.043 2 03050 Proteasome
0.025 1 00970 Aminoacyl-tRNA biosynthesis
0.015 1 04120 Ubiquitin mediated proteolysis

Select a plant to compare co-expressed genes between species.
Glycine_max
Hordeum_vulgare
Oryza_sativa
Populus_trichocarpa
Triticum_aestivum
Vitis_vinifera
Zea_mays