How to fix margins of tables

Question

Requesting help... Dear all, I have 2 questions if you could please help solve.

(1) Would anyone please be able to let me know a way to get this table within the margins of the document? Right now, the heading of the second column seems too wide. May be if you can suggest a way that I can shrink the header for the second column down to two lines, it might work. Please see image 1 attached. I have used the following code (please see the code below):

\begin{table}[H]
   \caption{Summary of gene inputs and pathway outputs for pathway analysis of the isografts}
   \small
   \centering
    \begin{tabular}{lllp{\dimexpr 0.65\linewidth-8\tabcolsep}}
   \toprule[\heavyrulewidth]\toprule[\heavyrulewidth]
   \textbf{Timepoint comparison} & \textbf{Total number of input genes (P < 0.01)} & \textbf{Pathway outputs} & \textbf{Number of statistically significant enriched pathways (P < 0.05)}\\ 
   \midrule
T0-T1g downregulated & 2308 & Immunological & 0\\
& & Inflammatory & 2 \\
T0-T1g upregulated & 2187 & Immunological & 14 \\
& & Inflammatory & 28 \\
T1g-T7g downregulated & 2034 & Immunological & 1\\
& & Inflammatory & 15 \\
T1g-T7g upregulated & 1897 & Immunological & 1\\
& & Inflammatory & 2 \\
T7g-T30g downregulated & 1360 & Immunological & 3\\
& & Inflammatory & 2 \\
T7g-T30g upregulated & 751 & Immunological & 4\\
& & Inflammatory & 8 \\\hdashline
   \bottomrule[\heavyrulewidth] 
   \end{tabular}
\end{table}

(2) Similar issue as the previous table, except this time, the header of the second column is in two lines, but doesn't align with the rest of the column. Would anyone please be able to let me know a way to align the header with rest of the content in the column? Please see image 2 attached.I have used the following code (please see the code below):

\begin{table}[H]
\setlength{\tabcolsep}{2.5pt}
   \caption{Serum markers in the allograft recipients with no significant difference in concentrations between timepoints}
   \small
    \centering
   \begin{tabular}{ l p{\dimexpr 0.65\linewidth-2\tabcolsep}}
   \toprule[\heavyrulewidth]\toprule[\heavyrulewidth]
   \textbf{Serum marker} & \textbf{\makecell {Limit of Detection (LOD)\\(pg/mL)}}\\ 
   \midrule
1.  AR (amphiregulin) & 13.6\\ 
2.  B7-1 (CD80) & 35.3\\ 
3.  BAFF-R (B cell activating factor receptor)  & 7.7\\ 
4.  BTC (betacellulin)  & 5.7\\ 
5.  C5a (complement C5 alpha chain) & 1.7\\ 
6.  CCL6    (C-C motif chemokine 6) & 23.2\\ 
7.  CD6 (T cell differentiation antigen 6)  & 2.5\\ 
8.  CX3CL1 (Fractalkine)    & 2016.3\\ 
32. Marapsin & 77.7\\\hdashline
   \bottomrule[\heavyrulewidth] 
   \end{tabular}
\end{table}

Please see the following details about some parameters I have used for the code as it may help;

\documentclass[12pt, a4paper]{report}
\input{Packages.tex} included the following;
% For tables
\usepackage{threeparttable}
\usepackage{threeparttablex}
\usepackage{ctable}
\usepackage{tabularx}
\usepackage{rotating}
\usepackage{makecell}
\usepackage{longtable}

% other
\usepackage[T1]{fontenc}
\usepackage[latin1]{inputenc}
\usepackage[english]{babel}
\usepackage{siunitx}
\usepackage{graphicx}
\usepackage{tipa} % for the \ark{} command
\usepackage{graphics} % for pdf, bitmapped graphics files
\usepackage{times} % assumes new font selection scheme installed
\usepackage{amsmath}
\usepackage{latexsym}
\usepackage{amscd}% for commutative diagrams
\usepackage{mathrsfs} %this package is for the script font \mathscr
\usepackage{relsize}
\usepackage{delarray}
\usepackage{pstricks}
\usepackage{theorem}
\usepackage{changepage}
\usepackage{euscript}
\usepackage{textcomp}
\usepackage{esvect}
\usepackage{parskip}
\usepackage{placeins}
\usepackage{subfigure}

Answer 1

Edit:* Now both tables:

With use of tabularray package with libraries booktabs and siunitx:

\documentclass[12pt, a4paper]{report}
\usepackage{geometry}
\usepackage[T1]{fontenc}
\usepackage{newtxtext} 
\usepackage{tabularray}
\UseTblrLibrary{booktabs, siunitx}
  \ExplSyntaxOn
\NewChildSelector{eachtwo}
  {
    \int_step_inline:nnnn {2}{2}{\l_tblr_childs_total_tl}
      { \clist_put_right:Nn \l_tblr_childs_clist {##1} }
  }
\ExplSyntaxOff
\begin{document}
\begin{table}[ht]
   \caption{Summary of gene inputs and pathway outputs for pathway analysis of the isografts}
\begin{tblr}{colsep  = 3pt,
             colspec = {@{} l
                        X[0.8, c, si={table-format=4.0}] 
                        l
                        X[1.2, c, si={table-format=2.0}]
                        @{}},
            rowsep = 0.5pt,
            row{1} = {font=\small\bfseries, m},
            row{eachtwo} = {abovesep=1ex},
            }
   \toprule
{Timepoint\ comparison}
    & {{{Total number\ of input genes $(P<0.01)$}}} 
        & {{{Pathway\ outputs}}} 
            & {{{No. of statistically significant enriched pathways $(P<0.05)$}}}\
   \midrule
T0-T1g downregulated 
    & 2308  & Immunological & 0             \
    &       & Inflammatory  & 2             \
T0-T1g upregulated 
    & 2187  & Immunological & 14            \
    &       & Inflammatory  & 28            \
T1g-T7g downregulated 
    & 2034  & Immunological & 1             \
    &       & Inflammatory  & 15            \
T1g-T7g upregulated 
    & 1897  & Immunological & 1             \
    &       & Inflammatory  & 2             \
T7g-T30g downregulated 
    & 1360  & Immunological & 3             \
    &       & Inflammatory  & 2             \
T7g-T30g upregulated 
    & 751   & Immunological & 4             \
    &       & Inflammatory  & 8             \
   \bottomrule
   \end{tblr}
\end{table}
\begin{table}[ht]
   \caption{Serum markers in the allograft recipients with no significant difference in concentrations between timepoints}
\begin{tblr}{colspec = {c
                        X[l]
                        Q[c, si={table-format=4.1}]
                        },
            rowsep = 0.5pt,
            row{1} = {font=\small\bfseries, c, m},
            row{eachtwo} = {abovesep=1ex},
            }
   \toprule
{Serum\ marker}
    & \SetCell[c=2]{c}  {Limit of Detection (LOD)\ (pg/mL)}
                            &           \
   \midrule

&   AR (amphiregulin)   & 13.6      \
&   B7-1 (CD80)         & 35.3      \
&   BAFF-R (B cell activating factor receptor)
                        & 7.7       \
&   BTC (betacellulin)  & 5.7       \
&   C5a (complement C5 alpha chain)
                        & 1.7       \
&   CCL6    (C-C motif chemokine 6)
                        & 23.2      \
&   CD6 (T cell differentiation antigen 6)
                        & 2.5       \
&   CX3CL1 (Fractalkine)& 2016.3    \
&   Marapsin            & 77.7      \
\bottomrule
\end{tblr}

\end{table}
\end{document}

Answer 2

In the first table, you need to allow automatic linebreaking in columns 2 thru 4. For both tables, I suggest you employ tabularx rather than tabular environments. I don't think it's necessary to bold-face the contents of the header cells. I would align the numeric data on their explicit or implicit decimal markers. Automatic row numbering in table 2 might also be desirable.

\documentclass{article}
\usepackage{booktabs}
\usepackage{tabularx} % for 'tabularx' env. and 'X' col. type
\usepackage{ragged2e} % for '\RaggedRight' and '\Centering' environment
\newcolumntype{L}{>{\RaggedRight}X} % raggedright version of 'X' col. type
\newcolumntype{C}{>{\Centering}X}   % centered version of 'X' col. type
\newcommand\mC[1]{\multicolumn{1}{C@{}}{#1}} % handy shortcut macro
\usepackage[per-mode=symbol]{siunitx}% for 'S' col. type and '\unit' macro
%% enable automatic row numbering in tables:
\newcounter{tblrow}[table]
\newcolumntype{t}{>{\refstepcounter{tblrow}\thetblrow.}r}
\begin{document}
\begin{table}[ht]
\setlength\tabcolsep{3pt} % default: 6pt
\caption{Summary of gene inputs and pathway outputs 
 for pathway analysis of the isografts}
\begin{tabularx}{\textwidth}{@{} l S[table-format=4.0] C S[table-format=4.1] @{}}
\toprule
Timepoint comparison & 
\mC{Total number of input genes ($P < 0.01$)} & 
Pathway outputs & 
\mC{Number of stat.\ sign.\ enriched pathways ($P < 0.05$)} \ 
\midrule
T0-T1g downregulated & 2308 & Immunological & 0\
& & Inflammatory & 2 \
T0-T1g upregulated & 2187 & Immunological & 14 \
& & Inflammatory & 28 \
\addlinespace
T1g-T7g downregulated & 2034 & Immunological & 1\
& & Inflammatory & 15 \
T1g-T7g upregulated & 1897 & Immunological & 1\
& & Inflammatory & 2 \
\addlinespace
T7g-T30g downregulated & 1360 & Immunological & 3\
& & Inflammatory & 2 \
T7g-T30g upregulated & 751 & Immunological & 4\
& & Inflammatory & 8 \   %%\hdashline
\bottomrule[\heavyrulewidth] 
\end{tabularx}
\bigskip\bigskip
\caption{Serum markers in the allograft recipients with no 
  significant difference in concentrations between timepoints}
\begin{tabularx}{\textwidth}{@{} t L S[table-format=4.1] @{}}
\toprule
% '\multicolumn{1}{@{}l}{}' serves to suppress display of row counter
\multicolumn{1}{@{}l}{} & Serum marker & {Limit of Detection (LOD)} \
\multicolumn{1}{@{}l}{} && {(\unit{\pico\gram\per\milli\liter}) } \ 
\midrule
& AR (amphiregulin) & 13.6\ 
& B7-1 (CD80) & 35.3\ 
& BAFF-R (B cell activating factor receptor)  & 7.7\ 
& BTC (betacellulin)  & 5.7\ 
& C5a (complement C5 alpha chain) & 1.7\ 
& CCL6    (C-C motif chemokine 6) & 23.2\ 
& CD6 (T cell differentiation antigen 6)  & 2.5\ 
& CX3CL1 (Fractalkine)    & 2016.3\

\multicolumn{1}{@{}r}{\setcounter{tblrow}{31}}& \dots \
& Marapsin & 77.7\ % reset value of 'tblrow' counter
\bottomrule 
\end{tabularx}
\end{table}
\end{document}