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Table 2 Fungal nitrogen-related DE genes from upregulated Basidiomycota. EBSeq [42, 43] was used to estimate posterior probability of differential expression (PPDE) ≥ 0.95. A full DE transcript list including expression data, functional description (if available), gene ontology terms (if available) and secondary annotation (if available) is provided in Additional file 6

From: Trees, fungi and bacteria: tripartite metatranscriptomics of a root microbiome responding to soil contamination

Query id Cont mean tpm Treat mean tpm FC 1° annotation id Subject description
c596378_g2_i3 0.14 66.39 477.06 gi|749759516|gb|KII84515.1| Ammonium transporter
c596378_g2_i2 0.14 64.18 458.91 tr|Q8NKD5|Q8NKD5_HEBCY Ammonium transporter
c599446_g2_i1 0.14 57.28 405.50 gi|660970957|gb|KEP54657.1| Rab GTPase family protein
c555426_g1_i1 0.04 47.83 1162.00 gi|646294952|gb|KDQ16118.1| Small GTPase-binding protein
c590384_g1_i3 0.36 47.03 130.17 tr|R7RZR8|R7RZR8_PUNST fun34-transmembrane protein of ammonia production
c597663_g1_i3 0.02 31.86 1277.49 tr|R7S8J0|R7S8J0_TRAVS Small GTPase-binding protein
c576075_g1_i1 0.02 22.26 1356.92 gi|691790442|emb|CDO74199.1| Amino acid transporter
c597663_g1_i1 0.01 20.67 2581.27 tr|V2X8E2|V2X8E2_MONRO Small GTPase-binding protein
c596122_g2_i1 0.00 18.08 4389.38 tr|V2WTU3|V2WTU3_MONRO Plasma membrane h(+)-atpase 1
c592122_g2_i1 0.00 18.00 inf tr|S7PWC9|S7PWC9_GLOTA Mitochondrial carrier
c598258_g3_i1 0.00 16.68 inf gi|597977025|ref.|XP_007362384.1| Urease
c597755_g1_i1 0.00 16.37 inf gi|754376368|gb|KIP08998.1| Subtilisin-like serine protease pepC
c601027_g2_i1 0.00 15.18 inf gi|660966237|gb|KEP50782.1| Serine carboxypeptidase
c590409_g1_i1 0.00 13.93 inf tr|E2LF88|E2LF88_MONPE Oligopeptide transporter
c602018_g3_i1 0.01 12.29 949.61 tr|R7S2N4|R7S2N4_PUNST Endopeptidase
c601958_g7_i1 0.00 11.68 inf tr|M2R776|M2R776_CERS8 Aminopeptidase 2
c597846_g2_i1 0.01 11.17 1682.64 gi|695572973|ref|XP_009551472.1| Purine transporter
c598346_g1_i1 0.00 10.15 inf gi|807753175|ref.|XP_012181382.1| ATP-dependent metallopeptidase Hfl
c596122_g2_i3 0.05 9.94 216.32 laccaria|A0A0C9XV60_9AGAR Plasma membrane ATPase
c600930_g1_i1 0.00 9.88 inf tr|V2X687|V2X687_MONRO Glutamate synthase
c575280_g1_i3 0.00 9.72 inf tr|F8NRP9|F8NRP9_SERL9 Oligopeptide transporter
c586208_g2_i4 0.00 9.42 inf gi|595766652|ref|XP_007261869.1| Small GTPase
c599446_g3_i1 0.00 8.68 inf tr|B0CRR7|B0CRR7_LACBS Ras-related protein Rab-5B
c597351_g5_i3 0.05 8.59 185.55 tr|D8PW94|D8PW94_SCHCM Carbon-nitrogen hydrolase
c600850_g1_i2 0.00 8.38 inf gi|751184086|gb|KIL70023.1| Aspartic peptidase A1
c591514_g1_i1 0.00 8.25 inf gi|597967903|ref.|XP_007360041.1| Ras protein
c600898_g1_i3 0.02 7.43 316.59 tr|M2RCY8|M2RCY8_CERS8 Zinc carboxypeptidase
c590849_g1_i2 0.00 7.23 inf gi|751185175|gb|KIL71111.1| Rab-type small GTP-binding protein
c594481_g1_i1 0.00 7.10 inf uniparc|UPI000444A56C Amino acid transporter
c595033_g1_i1 0.00 7.06 inf tr|V2WPM3|V2WPM3_MONRO Ras GTPase-activating protein
c596094_g1_i2 0.00 6.76 inf gi|695535578|ref|XP_009541732.1| Metallo peptidase M16B
c601513_g2_i5 0.00 6.72 inf tr|M2PP80|M2PP80_CERS8 Glutamine synthetase
c587799_g1_i1 0.00 5.74 inf laccaria|B0CVJ7|B0CVJ7_LACBS Aspartic peptidase A1
c583462_g2_i3 0.00 5.67 inf tr|A8N171|A8N171_COPC7 Glutathione transporter
c570564_g1_i1 0.00 5.19 inf gi|827762056|gb|KLO16666.1| Zn-dependent exopeptidase
c594381_g2_i2 0.00 5.13 inf gi|599097713|ref.|XP_007380030.1| Zn-dependent exopeptidase
c600158_g1_i5 0.03 5.12 203.31 tr|F8NFV4|F8NFV4_SERL9 rab GDP-dissociation inhibitor
c583177_g1_i2 0.00 4.84 inf gi|751693001|gb|KIM42985.1| Transmembrane GTPase fzo1
c600177_g1_i1 0.00 4.71 inf gi|914260206|gb|KNZ75358.1| Peptide/nitrate transporter
c601958_g3_i1 0.00 4.68 inf tr|M2R776|M2R776_CERS8 Aminopeptidase 2
c594481_g1_i2 0.00 4.50 inf gi|618814194|ref.|XP_007309736.1| Amino acid transporter
c567674_g1_i1 0.00 4.48 inf gi|599098740|ref.|XP_007380368.1| Carbon-nitrogen hydrolase
c597783_g1_i3 0.00 4.45 inf tr|F8QHR7|F8QHR7_SERL3 Glutamate carboxypeptidase
c594170_g1_i2 0.00 3.78 inf gi|751737188|gb|KIM85475.1| Mitochondrial carrier
c601872_g2_i1 0.00 3.76 inf gi|628824529|ref|XP_007762568.1| ATP-dependent metallopeptidase Hfl
c599577_g1_i2 0.00 3.73 inf gi|597902114|ref.|XP_007298356.1| Peptidase M24A methionine aminopeptidase
c602154_g2_i2 0.01 3.51 328.31 gi|761927343|gb|KIY48481.1| D-aspartate oxidase
c600522_g1_i1 0.00 3.41 inf gi|695555686|ref.|XP_009546958.1| Bleomycin hydrolases/aminopeptidases (cys family)
c598679_g1_i2 0.00 3.40 852.70 tr|M2QPL6|M2QPL6_CERS8 Aspartic-type endopeptidase
c601070_g1_i3 0.00 3.26 inf gi|599098141|ref|XP_007380172.1| Amine oxidase
c595365_g1_i2 0.00 2.95 inf tr|E2LXQ1|E2LXQ1_MONPE Amino acid transporter
c601230_g1_i3 0.01 2.92 561.26 gi|695571495|ref|XP_009551148.1| Metallo peptidase M24B
c600602_g1_i1 0.00 2.84 inf gi|695544112|ref.|XP_009543978.1| Small monomeric GTPase
c601825_g4_i5 0.00 2.32 inf gi|754370636|gb|KIP03412.1| Vacuolar amino acid transporter