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Lupus Nephritis Supp Table 5

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Supplementary Table 5 : Transcripts and DAVID pathways correlating with the expression of CD4 in lupus kidney biopsies Positive correlation Negative correlation Transcripts Pathways Transcripts Pathways Identifier Gene Symbol Correlation coefficient with CD4 Annotation Cluster 1 Enrichment Score: 26.47 Count P_Value Benjamini Identifier Gene Symbol Correlation coefficient with CD4 Annotation Cluster 1 Enrichment Score: 3.16 Count P_Value Benjamini ILMN_1727284 CD4 1 GOTERM_BP_FAT translational elongation 74 2.50E-42 1.00E-38 ILMN_1681389 C2H2 zinc finger protein-0.40001984 INTERPRO Ubiquitin-conjugating enzyme/RWD-like 17 2.00E-05 4.20E-02 ILMN_1772218 HLA-DPA1 0.934229063 SP_PIR_KEYWORDS ribosome 60 2.00E-41 4.60E-39 ILMN_1768954 RIBC1 -0.400186083 SMART UBCc 14 1.00E-04 3.50E-02 ILMN_1778977 TYROBP 0.933302249 KEGG_PATHWAY Ribosome 65 3.80E-35 6.60E-33 ILMN_1699190 SORCS1 -0.400223681 SP_PIR_KEYWORDS ubl conjugation pathway 81 1.30E-04 2.30E-02 ILMN_1689655 HLA-DRA 0.915891173 SP_PIR_KEYWORDS protein biosynthesis 91 4.10E-34 7.20E-32 ILMN_3249088 LOC93432 -0.400285215 GOTERM_MF_FAT small conjugating protein ligase activity 35 1.40E-04 4.40E-02 ILMN_3228688 HLA-DRB1 0.906190291 SP_PIR_KEYWORDS ribonucleoprotein 114 4.80E-34 6.70E-32 ILMN_1680436 CSH2 -0.400299744 SP_PIR_KEYWORDS ligase 54 1.50E-04 2.00E-02 ILMN_2157441 HLA-DRA 0.902996561 GOTERM_CC_FAT cytosolic ribosome 59 3.20E-33 2.30E-30 ILMN_1722755 KRTAP6-2 -0.400334007 GOTERM_MF_FAT acid-amino acid ligase activity 40 1.60E-04 4.00E-02 ILMN_2066066 HLA-DRB6 0.901531942 SP_PIR_KEYWORDS ribosomal protein 85 3.10E-29 3.60E-27 ILMN_3310171 MIR210 -0.400359894 INTERPRO Ubiquitin-conjugating enzyme, E2 14 2.10E-04 2.00E-01 ILMN_1736567 CD74 0.900464276 GOTERM_CC_FAT ribosomal subunit 70 6.50E-28 2.30E-25 ILMN_1799903 GALNTL1 -0.400392176 GOTERM_MF_FAT ubiquitin-protein ligase activity 31 3.60E-04 7.40E-02 ILMN_2366330 FERMT3 0.896532157 GOTERM_BP_FAT translation 122 6.60E-28 1.40E-24 ILMN_1754727 ARMCX5 -0.40044397 GOTERM_MF_FAT ligase activity, forming carbon-nitrogen bonds 43 3.90E-04 6.10E-02 ILMN_1815895 HLA-DRB1 0.895853418 GOTERM_CC_FAT cytosolic part 76 5.60E-27 1.30E-24 ILMN_1660020 LOC644662 -0.400562184 GOTERM_BP_FAT protein ubiquitination 25 1.40E-03 5.70E-01 ILMN_2379644 CD74 0.890964861 GOTERM_MF_FAT structural constituent of ribosome 79 6.80E-27 8.90E-24 ILMN_2369826 C16orf13 -0.400562661 GOTERM_BP_FAT protein modification by small protein conjugation 26 2.80E-03 6.00E-01 ILMN_2049536 TRPV2 0.889679914 GOTERM_CC_FAT ribonucleoprotein complex 160 2.50E-26 4.30E-24 ILMN_2206554 SLC35F5 -0.400563498 UP_SEQ_FEATURE active site:Glycyl thioester intermediate 16 4.70E-03 9.90E-01 ILMN_1718936 LST1 0.886044814 GOTERM_CC_FAT ribosome 90 7.50E-25 8.70E-23 ILMN_1853093 BG325888 -0.400578134 GOTERM_BP_FAT protein modification by small protein conjugation or removal 28 9.90E-03 8.80E-01 ILMN_1718558 PARP12 0.883825964 GOTERM_CC_FAT cytosolic small ribosomal subunit 30 1.80E-17 1.80E-15 ILMN_2331232 TNFRSF6B -0.400582848 KEGG_PATHWAY Ubiquitin mediated proteolysis 25 1.60E-02 7.80E-01 ILMN_3240316 TMSB4X 0.881816413 GOTERM_CC_FAT cytosolic large ribosomal subunit 29 3.10E-17 2.70E-15 ILMN_1700169 C15orf44 -0.400627977 GOTERM_CC_FAT ubiquitin ligase complex 16 5.60E-02 9.00E-01 ILMN_1683026 PSMB10 0.881679636 GOTERM_CC_FAT large ribosomal subunit 39 5.60E-17 8.70E-15 ILMN_1771689 EXD2 -0.400641297 Annotation Cluster 2 Enrichment Score: 2.83 Count P_Value Benjamini ILMN_2179837 BANF1 0.881663753 GOTERM_MF_FAT structural molecule activity 154 1.30E-15 5.80E-13 ILMN_1679134 NSMCE4A -0.400646612 GOTERM_BP_FAT dephosphorylation 41 5.20E-08 1.80E-04 ILMN_1786612 PSME2 0.881166328 GOTERM_CC_FAT small ribosomal subunit 32 7.30E-12 3.40E-10 ILMN_1838375 BM714348 -0.400665624 GOTERM_BP_FAT protein amino acid dephosphorylation 36 2.50E-07 4.40E-04 ILMN_1653828 CHFR 0.879799743 Annotation Cluster 2 Enrichment Score: 10.95 Count P_Value Benjamini ILMN_1653266 DNAJB14 -0.400749707 GOTERM_MF_FAT phosphoprotein phosphatase activity 41 4.70E-07 6.10E-04 ILMN_1754842 DLGAP4 0.875737515 GOTERM_CC_FAT intracellular non-membrane-bounded organelle 477 3.80E-16 2.30E-14 ILMN_1719316 TMED3 -0.400813303 GOTERM_MF_FAT phosphatase activity 54 6.40E-07 4.10E-04 ILMN_1668039 GYPC 0.874017008 GOTERM_CC_FAT non-membrane-bounded organelle 477 3.80E-16 2.30E-14 ILMN_3257233 AK126616 -0.400986267 GOTERM_MF_FAT protein tyrosine phosphatase activity 28 8.70E-06 3.70E-03 ILMN_1752340 ARF5 0.871364059 GOTERM_CC_FAT cytoskeleton 214 9.90E-03 1.30E-01 ILMN_1692276 GGPS1 -0.400992588 SP_PIR_KEYWORDS protein phosphatase 30 6.30E-05 1.40E-02 ILMN_1654319 HAPLN3 0.86967548 Annotation Cluster 3 Enrichment Score: 10.64 Count P_Value Benjamini ILMN_1790595 TFAP2E -0.401012982 UP_SEQ_FEATURE active site:Phosphocysteine intermediate 21 3.00E-04 7.30E-01 ILMN_2390299 PSMB8 0.868740369 GOTERM_CC_FAT intracellular organelle lumen 343 3.90E-14 2.50E-12 ILMN_1734559 SORD -0.401202426 INTERPRO Protein-tyrosine phosphatase, active site 22 3.20E-04 2.10E-01 Dual-specific/protein-tyrosine phosphatase, conserved ILMN_1747195 PSMB8 0.866391356 GOTERM_CC_FAT membrane-enclosed lumen 354 6.40E-14 3.70E-12 ILMN_1698731 SEC31B -0.401253836 INTERPRO region 20 7.80E-04 2.90E-01 ILMN_2176063 FCGR1C 0.866366101 GOTERM_CC_FAT organelle lumen 348 7.50E-14 4.10E-12 ILMN_1652333 FN3KRP -0.401355089 SMART PTPc 12 1.30E-03 2.10E-01 ILMN_2111739 MAN2C1 0.866279082 GOTERM_CC_FAT nuclear lumen 284 1.90E-12 9.40E-11 ILMN_2052863 RNF5 -0.401425107 INTERPRO Protein-tyrosine phosphatase 19 1.80E-03 4.80E-01 ILMN_1807277 IFI30 0.86456805 GOTERM_CC_FAT nucleoplasm 170 3.50E-07 1.50E-05 ILMN_3311095 MIR643 -0.401427458 INTERPRO Protein-tyrosine phosphatase, receptor/non-receptor type 12 2.30E-03 5.20E-01 ILMN_1794473 PHF17 0.863368562 GOTERM_CC_FAT nucleolus 138 1.30E-06 4.90E-05 ILMN_1663263 EPHA10 -0.401468095 UP_SEQ_FEATURE domain:Tyrosine-protein phosphatase 13 2.60E-02 1.00E+00 ILMN_1758250 TRAFD1 0.862805609 Annotation Cluster 4 Enrichment Score: 6.84 Count P_Value Benjamini ILMN_3255211 KIAA2015 -0.401494305 GOTERM_MF_FAT protein tyrosine/serine/threonine phosphatase activity 10 4.00E-02 8.30E-01 ILMN_1772359 LAPTM5 0.862504464 SP_PIR_KEYWORDS ubl conjugation 117 4.10E-08 2.20E-06 ILMN_1676548 BZW2 -0.401528449 SP_PIR_KEYWORDS tyrosine-specific phosphatase 7 9.90E-02 8.40E-01 cross-link:Glycyl lysine isopeptide (Lys-Gly) (interchain with G- ILMN_1679809 GSTP1 0.861629683 UP_SEQ_FEATURE Cter in ubiquitin) 53 4.50E-08 8.10E-05 ILMN_1709020 MYBL2 -0.401560655 SP_PIR_KEYWORDS phosphoric monoester hydrolase 12 1.00E-01 8.30E-01 ILMN_1651788 MAP3K11 0.861566346 SP_PIR_KEYWORDS isopeptide bond 69 1.70E-06 5.80E-05 ILMN_1651341 LOC401010 -0.40162232 INTERPRO Dual specificity phosphatase, catalytic domain 8 1.10E-01 1.00E+00 ILMN_1778360 PYGB 0.861254289 Annotation Cluster 5 Enrichment Score: 5.35 Count P_Value Benjamini ILMN_3285238 BX537874 -0.40162554 INTERPRO Protein-tyrosine phosphatase, dual specificity 7 1.90E-01 1.00E+00 ILMN_2349658 TSPO 0.860302388 GOTERM_BP_FAT macromolecular complex assembly 136 1.00E-07 7.20E-05 ILMN_1701239 SPRR2E -0.401647677 GOTERM_MF_FAT transmembrane receptor protein phosphatase activity 4 3.00E-01 9.90E-01 ILMN_1740015 CD14 0.858368684 GOTERM_BP_FAT macromolecular complex subunit organization 138 1.70E-06 3.10E-04 ILMN_2288290 CDY1B -0.4017477 UP_SEQ_FEATURE domain:Tyrosine-protein phosphatase 2 3 3.60E-01 1.00E+00 ILMN_1760683 SRSF9 0.857616844 GOTERM_BP_FAT cellular macromolecular complex assembly 73 2.10E-06 3.20E-04 ILMN_1674297 HCFC2 -0.401754371 UP_SEQ_FEATURE domain:Tyrosine-protein phosphatase 1 3 3.60E-01 1.00E+00 ILMN_2062468 IGFBP7 0.857204295 GOTERM_BP_FAT cellular macromolecular complex subunit organization 77 1.20E-05 1.20E-03 ILMN_1769071 XKRX -0.40180268 SMART DSPc 3 8.00E-01 1.00E+00 ILMN_1715024 LSS 0.857094666 GOTERM_BP_FAT protein complex assembly 99 4.10E-05 3.20E-03 ILMN_1773968 SERBP1 -0.401804507 Annotation Cluster 3 Enrichment Score: 2.62 Count P_Value Benjamini ILMN_1723706 GRAMD4 0.856571802 GOTERM_BP_FAT protein complex biogenesis 99 4.10E-05 3.20E-03 ILMN_2222163 HIST1H3B -0.401887856 SP_PIR_KEYWORDS ubl conjugation pathway 81 1.30E-04 2.30E-02 ILMN_1782057 ATP8B2 0.855792595 Annotation Cluster 6 Enrichment Score: 4.78 Count P_Value Benjamini ILMN_1781672 GAB1 -0.401901556 GOTERM_BP_FAT modification-dependent protein catabolic process 88 3.50E-04 2.70E-01 ILMN_2366041 ITM2C 0.855750662 SP_PIR_KEYWORDS mrna splicing 54 8.30E-08 3.90E-06 ILMN_1660852 ZC3H6 -0.401907906 GOTERM_BP_FAT modification-dependent macromolecule catabolic process 88 3.50E-04 2.70E-01 ILMN_1761464 CD74 0.854043623 SP_PIR_KEYWORDS mrna processing 61 4.30E-07 1.70E-05 ILMN_1736045 KCNJ16 -0.401981532 GOTERM_BP_FAT proteolysis involved in cellular protein catabolic process 88 1.40E-03 5.20E-01 ILMN_1689968 PLEKHO2 0.853935274 GOTERM_BP_FAT RNA splicing 69 4.80E-07 2.20E-04 ILMN_2389528 MTL5 -0.401986801 GOTERM_BP_FAT cellular protein catabolic process 88 1.70E-03 5.20E-01 ILMN_1680453 ITM2C 0.853816711 GOTERM_BP_FAT RNA processing 114 4.80E-07 2.00E-04 ILMN_1805842 FHL1 -0.401998765 GOTERM_BP_FAT cellular macromolecule catabolic process 102 2.30E-03 6.00E-01 ILMN_1691892 TAGLN2 0.853601352 GOTERM_BP_FAT mRNA metabolic process 83 1.00E-06 2.40E-04 ILMN_1791702 SMARCA2 -0.402008017 GOTERM_BP_FAT protein catabolic process 88 4.00E-03 6.70E-01 ILMN_1683271 TMSB4X 0.853486495 GOTERM_BP_FAT mRNA processing 74 1.50E-06 2.90E-04 ILMN_1806022 RNF212 -0.402016792 GOTERM_BP_FAT macromolecule catabolic process 106 5.70E-03 7.40E-01 ILMN_1785005
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    bioRxiv preprint doi: https://doi.org/10.1101/2020.01.19.905109; this version posted January 19, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Dual Proteome-scale Networks Reveal Cell-specific Remodeling of the Human Interactome Edward L. Huttlin1*, Raphael J. Bruckner1,3, Jose Navarrete-Perea1, Joe R. Cannon1,4, Kurt Baltier1,5, Fana Gebreab1, Melanie P. Gygi1, Alexandra Thornock1, Gabriela Zarraga1,6, Stanley Tam1,7, John Szpyt1, Alexandra Panov1, Hannah Parzen1,8, Sipei Fu1, Arvene Golbazi1, Eila Maenpaa1, Keegan Stricker1, Sanjukta Guha Thakurta1, Ramin Rad1, Joshua Pan2, David P. Nusinow1, Joao A. Paulo1, Devin K. Schweppe1, Laura Pontano Vaites1, J. Wade Harper1*, Steven P. Gygi1*# 1Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA. 2Broad Institute, Cambridge, MA, 02142, USA. 3Present address: ICCB-Longwood Screening Facility, Harvard Medical School, Boston, MA, 02115, USA. 4Present address: Merck, West Point, PA, 19486, USA. 5Present address: IQ Proteomics, Cambridge, MA, 02139, USA. 6Present address: Vor Biopharma, Cambridge, MA, 02142, USA. 7Present address: Rubius Therapeutics, Cambridge, MA, 02139, USA. 8Present address: RPS North America, South Kingstown, RI, 02879, USA. *Correspondence: [email protected] (E.L.H.), [email protected] (J.W.H.), [email protected] (S.P.G.) #Lead Contact: [email protected] bioRxiv preprint doi: https://doi.org/10.1101/2020.01.19.905109; this version posted January 19, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder.
  • PROTEOMIC ANALYSIS of HUMAN URINARY EXOSOMES. Patricia

    PROTEOMIC ANALYSIS of HUMAN URINARY EXOSOMES. Patricia

    ABSTRACT Title of Document: PROTEOMIC ANALYSIS OF HUMAN URINARY EXOSOMES. Patricia Amalia Gonzales Mancilla, Ph.D., 2009 Directed By: Associate Professor Nam Sun Wang, Department of Chemical and Biomolecular Engineering Exosomes originate as the internal vesicles of multivesicular bodies (MVBs) in cells. These small vesicles (40-100 nm) have been shown to be secreted by most cell types throughout the body. In the kidney, urinary exosomes are released to the urine by fusion of the outer membrane of the MVBs with the apical plasma membrane of renal tubular epithelia. Exosomes contain apical membrane and cytosolic proteins and can be isolated using differential centrifugation. The analysis of urinary exosomes provides a non- invasive means of acquiring information about the physiological or pathophysiological state of renal cells. The overall objective of this research was to develop methods and knowledge infrastructure for urinary proteomics. We proposed to conduct a proteomic analysis of human urinary exosomes. The first objective was to profile the proteome of human urinary exosomes using liquid chromatography-tandem spectrometry (LC- MS/MS) and specialized software for identification of peptide sequences from fragmentation spectra. We unambiguously identified 1132 proteins. In addition, the phosphoproteome of human urinary exosomes was profiled using the neutral loss scanning acquisition mode of LC-MS/MS. The phosphoproteomic profiling identified 19 phosphorylation sites corresponding to 14 phosphoproteins. The second objective was to analyze urinary exosomes samples isolated from patients with genetic mutations. Polyclonal antibodies were generated to recognize epitopes on the gene products of these genetic mutations, NKCC2 and MRP4. The potential usefulness of urinary exosome analysis was demonstrated using the well-defined renal tubulopathy, Bartter syndrome type I and using the single nucleotide polymorphism in the ABCC4 gene.
  • Exploring the Metastatic Role of the Inhibitor of Apoptosis BIRC6 in Breast Cancer

    Exploring the Metastatic Role of the Inhibitor of Apoptosis BIRC6 in Breast Cancer

    bioRxiv preprint doi: https://doi.org/10.1101/2021.04.08.438518; this version posted April 10, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Exploring the metastatic role of the inhibitor of apoptosis BIRC6 in Breast 2 Cancer 3 Corresponding author: Matias Luis Pidre, Pringles 3010, Lanús, Buenos Aires, Argentina, CP 1824 4 [email protected], mobile: +54 9 221 364 6836 5 AUTHORS 6 Santiago M. Gómez Bergna1; Abril Marchesini1; Leslie C. Amorós Morales1; Paula N. Arrías1; Hernán 7 G. Farina2; Víctor Romanowski1; M. Florencia Gottardo2*; Matias L. Pidre1*. 8 *Both authors equally contributed to this work. 9 AUTHOR AFFILIATIONS 10 1Instituto de Biotecnología y biología molecular (IBBM-CONICET-UNLP) 11 2Center of Molecular & Translational Oncology, Department of Science and Technology, 12 National University of Quilmes, Buenos Aires, Argentina. 13 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.04.08.438518; this version posted April 10, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 14 Abstract 15 Breast cancer is the most common cancer as well as the first cause of death by cancer in 16 women worldwide. BIRC6 (baculoviral IAP repeat-containing protein 6) is a member of the 17 inhibitors of apoptosis protein family thought to play an important role in the progression or 18 chemoresistance of many cancers. The aim of the present work was to investigate the role of 19 apoptosis inhibitor BIRC6 in breast cancer, focusing particularly on its involvement in the 20 metastatic cascade.
  • ONLINE SUPPLEMENTARY TABLE Table 2. Differentially Expressed

    ONLINE SUPPLEMENTARY TABLE Table 2. Differentially Expressed

    ONLINE SUPPLEMENTARY TABLE Table 2. Differentially Expressed Probe Sets in Livers of GK Rats. A. Immune/Inflammatory (67 probe sets, 63 genes) Age Strain Probe ID Gene Name Symbol Accession Gene Function 5 WKY 1398390_at small inducible cytokine B13 precursor Cxcl13 AA892854 chemokine activity; lymph node development 5 WKY 1389581_at interleukin 33 Il33 BF390510 cytokine activity 5 WKY *1373970_at interleukin 33 Il33 AI716248 cytokine activity 5 WKY 1369171_at macrophage stimulating 1 (hepatocyte growth factor-like) Mst1; E2F2 NM_024352 serine-throenine kinase; tumor suppression 5 WKY 1388071_x_at major histocompatability antigen Mhc M24024 antigen processing and presentation 5 WKY 1385465_at sialic acid binding Ig-like lectin 5 Siglec5 BG379188 sialic acid-recognizing receptor 5 WKY 1393108_at major histocompatability antigen Mhc BM387813 antigen processing and presentation 5 WKY 1388202_at major histocompatability antigen Mhc BI395698 antigen processing and presentation 5 WKY 1371171_at major histocompatability antigen Mhc M10094 antigen processing and presentation 5 WKY 1370382_at major histocompatability antigen Mhc BI279526 antigen processing and presentation 5 WKY 1371033_at major histocompatability antigen Mhc AI715202 antigen processing and presentation 5 WKY 1383991_at leucine rich repeat containing 8 family, member E Lrrc8e BE096426 proliferation and activation of lymphocytes and monocytes. 5 WKY 1383046_at complement component factor H Cfh; Fh AA957258 regulation of complement cascade 4 WKY 1369522_a_at CD244 natural killer